book.bib

@article{Prjibelski.2020, 
year = {2020}, 
title = {{Using SPAdes De Novo Assembler}}, 
author = {Prjibelski, Andrey and Antipov, Dmitry and Meleshko, Dmitry and Lapidus, Alla and Korobeynikov, Anton}, 
journal = {Current Protocols in Bioinformatics}, 
issn = {1934-3396}, 
doi = {10.1002/cpbi.102}, 
pmid = {32559359}, 
abstract = {{SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single‐cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole‐genome sequencing and metagenomic datasets. In addition, we present guidelines for understanding results with use cases for each pipeline, and several additional support protocols that help in using SPAdes properly. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Assembling isolate bacterial datasets Basic Protocol 2: Assembling metagenomic datasets Basic Protocol 3: Assembling sets of putative plasmids Basic Protocol 4: Assembling transcriptomes Basic Protocol 5: Assembling putative biosynthetic gene clusters Support Protocol 1: Installing SPAdes Support Protocol 2: Providing input via command line Support Protocol 3: Providing input data via YAML format Support Protocol 4: Restarting previous run Support Protocol 5: Determining strand‐specificity of RNA‐seq data}}, 
pages = {e102}, 
number = {1}, 
volume = {70}
}
@article{Tennessen.2016, 
year = {2016}, 
title = {{ProDeGe: a computational protocol for fully automated decontamination of genomes}}, 
author = {Tennessen, Kristin and Andersen, Evan and Clingenpeel, Scott and Rinke, Christian and Lundberg, Derek S and Han, James and Dangl, Jeff L and Ivanova, Natalia and Woyke, Tanja and Kyrpides, Nikos and Pati, Amrita}, 
journal = {The ISME Journal}, 
issn = {1751-7362}, 
doi = {10.1038/ismej.2015.100}, 
pmid = {26057843}, 
pmcid = {PMC4681846}, 
abstract = {{Single amplified genomes and genomes assembled from metagenomes have enabled the exploration of uncultured microorganisms at an unprecedented scale. However, both these types of products are plagued by contamination. Since these genomes are now being generated in a high-throughput manner and sequences from them are propagating into public databases to drive novel scientific discoveries, rigorous quality controls and decontamination protocols are urgently needed. Here, we present ProDeGe (Protocol for fully automated Decontamination of Genomes), the first computational protocol for fully automated decontamination of draft genomes. ProDeGe classifies sequences into two classes—clean and contaminant—using a combination of homology and feature-based methodologies. On average, 84\% of sequence from the non-target organism is removed from the data set (specificity) and 84\% of the sequence from the target organism is retained (sensitivity). The procedure operates successfully at a rate of \textbackslashtextasciitilde0.30 CPU core hours per megabase of sequence and can be applied to any type of genome sequence.}}, 
pages = {269--272}, 
number = {1}, 
volume = {10}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Tennessen/Tennessen_2016.pdf}
}
@article{Uritskiy.2018, 
year = {2018}, 
title = {{MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis}}, 
author = {Uritskiy, Gherman V. and DiRuggiero, Jocelyne and Taylor, James}, 
journal = {Microbiome}, 
doi = {10.1186/s40168-018-0541-1}, 
pmid = {30219103}, 
abstract = {{The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. Extracting individual draft genomes (bins) facilitates metagenomic analysis at the single genome level. Software and pipelines for such analysis have become diverse and sophisticated, resulting in a significant burden for biologists to access and use them. Furthermore, while bin extraction algorithms are rapidly improving, there is still a lack of tools for their evaluation and visualization. To address these challenges, we present metaWRAP, a modular pipeline software for shotgun metagenomic data analysis. MetaWRAP deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. MetaWRAP is flexible enough to give investigators control over the analysis, while still being easy-to-install and easy-to-use. It includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly. MetaWRAP’s hybrid bin extraction algorithm outperforms individual binning approaches and other bin consolidation programs in both synthetic and real data sets. Finally, metaWRAP comes with numerous modules for the analysis of metagenomic bins, including taxonomy assignment, abundance estimation, functional annotation, and visualization. MetaWRAP is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomic bins. The bin refinement and reassembly modules of metaWRAP consistently outperform other binning approaches. Each module of metaWRAP is also a standalone component, making it a flexible and versatile tool for tackling metagenomic shotgun sequencing data. MetaWRAP is open-source software available at https://github.com/bxlab/metaWRAP.}}, 
pages = {158}, 
number = {1}, 
volume = {6}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Uritskiy/Uritskiy_2018.pdf}
}
@article{Li.2013, 
year = {2013}, 
title = {{Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM}}, 
author = {Li, Heng}, 
journal = {arXiv}, 
eprint = {1303.3997}, 
abstract = {{Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads and performs chimeric alignment. The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases. For mapping 100bp sequences, BWA-MEM shows better performance than several state-of-art read aligners to date. Availability and implementation: BWA-MEM is implemented as a component of BWA, which is available at http://github.com/lh3/bwa. Contact: hengli@broadinstitute.org}}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Li/Li_2013.pdf}
}
@article{Wagner.2012, 
year = {2012}, 
title = {{Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples}}, 
author = {Wagner, Günter P. and Kin, Koryu and Lynch, Vincent J.}, 
journal = {Theory in Biosciences}, 
issn = {1431-7613}, 
doi = {10.1007/s12064-012-0162-3}, 
pmid = {22872506}, 
abstract = {{Measures of RNA abundance are important for many areas of biology and often obtained from high-throughput RNA sequencing methods such as Illumina sequence data. These measures need to be normalized to remove technical biases inherent in the sequencing approach, most notably the length of the RNA species and the sequencing depth of a sample. These biases are corrected in the widely used reads per kilobase per million reads (RPKM) measure. Here, we argue that the intended meaning of RPKM is a measure of relative molar RNA concentration (rmc) and show that for each set of transcripts the average rmc is a constant, namely the inverse of the number of transcripts mapped. Further, we show that RPKM does not respect this invariance property and thus cannot be an accurate measure of rmc. We propose a slight modification of RPKM that eliminates this inconsistency and call it TPM for transcripts per million. TPM respects the average invariance and eliminates statistical biases inherent in the RPKM measure.}}, 
pages = {281--285}, 
number = {4}, 
volume = {131}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Wagner/Wagner_2012.pdf}
}
@article{Khadka.2018, 
year = {2018}, 
title = {{Evolutionary History of Copper Membrane Monooxygenases}}, 
author = {Khadka, Roshan and Clothier, Lindsay and Wang, Lin and Lim, Chee Kent and Klotz, Martin G. and Dunfield, Peter F.}, 
journal = {Frontiers in Microbiology}, 
issn = {1664-302X}, 
doi = {10.3389/fmicb.2018.02493}, 
pmid = {30420840}, 
abstract = {{Copper membrane monooxygenases (CuMMOs) oxidize ammonia, methane and some short-chain alkanes and alkenes. They are encoded by three genes, usually in an operon of xmoCAB. We aligned xmo operons from 66 microbial genomes, including members of the Alpha-, Beta-, and Gamma-proteobacteria, Verrucomicrobia, Actinobacteria, Thaumarchaeota and the candidate phylum NC10. Phylogenetic and compositional analyses were used to reconstruct the evolutionary history of the enzyme and detect potential lateral gene transfer (LGT) events. The phylogenetic analyses showed at least 10 clusters corresponding to a combination of substrate specificity and bacterial taxonomy, but with no overriding structure based on either function or taxonomy alone. Adaptation of the enzyme to preferentially oxidize either ammonia or methane has occurred more than once. Individual phylogenies of all three genes, xmoA, xmoB and xmoC, closely matched, indicating that this operon evolved or was consistently transferred as a unit, with the possible exception of the methane monooxygenase operons in Verrucomicrobia, where the pmoB gene has a distinct phylogeny from pmoA and pmoC. Compositional analyses indicated that some clusters of xmoCAB operons (for example, the pmoCAB in gammaproteobacterial methanotrophs and the amoCAB in betaproteobacterial nitrifiers) were compositionally very different from their genomes, possibly indicating recent lateral transfer of these operons. The combined phylogenetic and compositional analyses support the hypothesis that an ancestor of the nitrifying bacterium Nitrosococcus was the donor of methane monooxygenase (pMMO) to both the alphaproteobacterial and gammaproteobacterial methanotrophs, but that before this event the gammaproteobacterial methanotrophs originally possessed another CuMMO (Pxm), which has since been lost in many species.}}, 
pages = {2493}, 
volume = {9}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Khadka/Khadka_2018.pdf}
}
@article{Li.2015, 
year = {2015}, 
title = {{MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph}}, 
author = {Li, Dinghua and Liu, Chi-Man and Luo, Ruibang and Sadakane, Kunihiko and Lam, Tak-Wah}, 
journal = {Bioinformatics}, 
issn = {1367-4803}, 
doi = {10.1093/bioinformatics/btv033}, 
pmid = {25609793}, 
abstract = {{Summary: MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252 Gbps in 44.1 and 99.6 h on a single computing node with and without a graphics processing unit, respectively. MEGAHIT assembles the data as a whole, i.e. no pre-processing like partitioning and normalization was needed. When compared with previous methods on assembling the soil data, MEGAHIT generated a three-time larger assembly, with longer contig N50 and average contig length; furthermore, 55.8\% of the reads were aligned to the assembly, giving a fourfold improvement. Availability and implementation: The source code of MEGAHIT is freely available at https://github.com/voutcn/megahit under GPLv3 license. Contact:rb@l3-bioinfo.com or twlam@cs.hku.hk Supplementary information: Supplementary data are available at Bioinformatics online.}}, 
pages = {1674--1676}, 
number = {10}, 
volume = {31}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Li/Li_2015.pdf}
}
@article{Bolger.2014, 
year = {2014}, 
title = {{Trimmomatic: a flexible trimmer for Illumina sequence data}}, 
author = {Bolger, Anthony M. and Lohse, Marc and Usadel, Bjoern}, 
journal = {Bioinformatics}, 
issn = {1367-4803}, 
doi = {10.1093/bioinformatics/btu170}, 
pmid = {24695404}, 
pmcid = {PMC4103590}, 
abstract = {{Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact:usadel@bio1.rwth-aachen.de Supplementary information:Supplementary data are available at Bioinformatics online.}}, 
pages = {2114--2120}, 
number = {15}, 
volume = {30}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Bolger/Bolger_2014.pdf}
}
@article{Letunic.2019, 
year = {2019}, 
title = {{Interactive Tree Of Life (iTOL) v4: recent updates and new developments}}, 
author = {Letunic, Ivica and Bork, Peer}, 
journal = {Nucleic Acids Research}, 
issn = {1362-4962}, 
doi = {10.1093/nar/gkz239}, 
pmid = {30931475}, 
abstract = {{The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. The current version introduces four new dataset types, together with numerous new features. Annotation options have been expanded and new control options added for many display elements. An interactive spreadsheet-like editor has been implemented, providing dataset creation and editing directly in the web interface. Font support has been rewritten with full support for UTF-8 character encoding throughout the user interface. Google Web Fonts are now fully supported in the tree text labels. iTOL v4 is the first tool which supports direct visualization of Qiime 2 trees and associated annotations. The user account system has been streamlined and expanded with new navigation options, and currently handles >700 000 trees from more than 40 000 individual users. Full batch access has been implemented allowing programmatic upload and export of trees and annotations.}}, 
pages = {gkz239--}, 
number = {W1}, 
volume = {47}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Letunic/Letunic_2019.pdf}
}
@article{Morgan-Lang.2020, 
year = {2020}, 
title = {{TreeSAPP: The Tree-based Sensitive and Accurate Phylogenetic Profiler}}, 
author = {Morgan-Lang, Connor and McLaughlin, Ryan and Armstrong, Zachary and Zhang, Grace and Chan, Kevin and Hallam, Steven J}, 
journal = {Bioinformatics}, 
issn = {1367-4803}, 
doi = {10.1093/bioinformatics/btaa588}, 
pmid = {32637989}, 
abstract = {{Abstract Motivation Microbial communities drive matter and energy transformations integral to global biogeochemical cycles, yet many taxonomic groups facilitating these processes remain poorly represented in biological sequence databases. Due to this missing information, taxonomic assignment of sequences from environmental genomes remains inaccurate. Results We present the Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software for functionally and taxonomically classifying genes, reactions and pathways from genomes of cultivated and uncultivated microorganisms using reference packages representing coding sequences mediating multiple globally relevant biogeochemical cycles. TreeSAPP uses linear regression of evolutionary distance on taxonomic rank to improve classifications, assigning both closely related and divergent query sequences at the appropriate taxonomic rank. TreeSAPP is able to provide quantitative functional and taxonomic classifications for both assembled and unassembled sequences and files supporting interactive tree of life visualizations. Availability and implementation TreeSAPP was developed in Python 3 as an open-source Python package and is available on GitHub at https://github.com/hallamlab/TreeSAPP. Supplementary information Supplementary data are available at Bioinformatics online.}}, 
pages = {btaa588--}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Morgan-Lang/Morgan-Lang_2020.pdf}
}
@article{Louca.2016, 
year = {2016}, 
title = {{Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone}}, 
author = {Louca, Stilianos and Hawley, Alyse K and Katsev, Sergei and Torres-Beltran, Monica and Bhatia, Maya P and Kheirandish, Sam and Michiels, Céline C and Capelle, David and Lavik, Gaute and Doebeli, Michael and Crowe, Sean A and Hallam, Steven J}, 
journal = {Proceedings of the National Academy of Sciences}, 
issn = {0027-8424}, 
doi = {10.1073/pnas.1602897113}, 
pmid = {27655888}, 
abstract = {{Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet—a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite “leakage” during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales.}}, 
pages = {E5925--E5933}, 
number = {40}, 
volume = {113}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Louca/Louca_2016.pdf}
}
@article{Hawley.2014, 
year = {2014}, 
title = {{Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes}}, 
author = {Hawley, A K and Brewer, H M and Norbeck, A D and Pa a-Toli , L and Hallam, S J}, 
journal = {Proceedings of the National Academy of Sciences}, 
issn = {0027-8424}, 
doi = {10.1073/pnas.1322132111}, 
pmid = {25053816}, 
pmcid = {PMC4128106}, 
abstract = {{Marine oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified waters. Currently OMZs are expanding due to global climate change with resulting feedback on marine ecosystem function. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally stratified fjord to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components for nitrification, anaerobic ammonium oxidation (anammox), denitrification, and inorganic carbon fixation were differentially expressed across the redoxcline and covaried with distribution patterns of ubiquitous OMZ microbes including Thaumarchaeota, Nitrospina, Nitrospira, Planctomycetes, and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters, and denitrification, sulfur oxidation, and inorganic carbon fixation pathways affiliated with the SUP05 group of nitrate-reducing sulfur oxidizers dominated suboxic and anoxic waters. Nitrifier nitrite oxidation and anammox pathways affiliated with Nirospina, Nitrospira, and Planctomycetes, respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The numerical abundance of SUP05 proteins mediating inorganic carbon fixation under anoxic conditions suggests that SUP05 will become increasingly important in global ocean carbon and nutrient cycling as OMZs expand.}}, 
pages = {11395--11400}, 
number = {31}, 
volume = {111}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Hawley/Hawley_2014.pdf}
}
@article{Torres-Beltrán.2017, 
year = {2017}, 
title = {{A compendium of geochemical information from the Saanich Inlet water column}}, 
author = {Torres-Beltrán, Mónica and Hawley, Alyse K. and Capelle, David and Zaikova, Elena and Walsh, David A. and Mueller, Andreas and Scofield, Melanie and Payne, Chris and Pakhomova, Larysa and Kheirandish, Sam and Finke, Jan and Bhatia, Maya and Shevchuk, Olena and Gies, Esther A. and Fairley, Diane and Michiels, Céline and Suttle, Curtis A. and Whitney, Frank and Crowe, Sean A. and Tortell, Philippe D. and Hallam, Steven J.}, 
journal = {Scientific Data}, 
doi = {10.1038/sdata.2017.159}, 
pmid = {29087371}, 
pages = {170159}, 
number = {1}, 
volume = {4}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Torres-Beltrán/Torres-Beltrán_2017.pdf}
}
@article{Hallam.2017, 
year = {2017}, 
title = {{Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone}}, 
author = {Hallam, Steven J. and Torres-Beltrán, Mónica and Hawley, Alyse K.}, 
journal = {Scientific Data}, 
issn = {2052-4463}, 
doi = {10.1038/sdata.2017.158}, 
pmid = {29087370}, 
abstract = {{Today in Scientific Data, two compendia of geochemical and multi-omic sequence information (DNA, RNA, protein) generated over almost a decade of time series monitoring in a seasonally anoxic coastal marine setting are presented to the scientific community. These data descriptors introduce a model ecosystem for the study of microbial responses to ocean deoxygenation, a phenotype that is currently expanding due to climate change. Public access to this time series information is intended to promote scientific collaborations and the generation of new hypotheses relevant to microbial ecology, biogeochemistry and global change issues.}}, 
pages = {170158}, 
number = {1}, 
volume = {4}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Hallam/Hallam_2017.pdf}
}
@article{Hawley.2017, 
year = {2017}, 
title = {{A compendium of multi-omic sequence information from the Saanich Inlet water column}}, 
author = {Hawley, Alyse K. and Torres-Beltrán, Mónica and Zaikova, Elena and Walsh, David A. and Mueller, Andreas and Scofield, Melanie and Kheirandish, Sam and Payne, Chris and Pakhomova, Larysa and Bhatia, Maya and Shevchuk, Olena and Gies, Esther A. and Fairley, Diane and Malfatti, Stephanie A. and Norbeck, Angela D. and Brewer, Heather M. and Pasa-Tolic, Ljiljana and Rio, Tijana Glavina del and Suttle, Curtis A. and Tringe, Susannah and Hallam, Steven J.}, 
journal = {Scientific Data}, 
doi = {10.1038/sdata.2017.160}, 
pmid = {29087368}, 
pages = {170160}, 
number = {1}, 
volume = {4}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Hawley/Hawley_2017.pdf}
}
@article{Parks.2015, 
year = {2015}, 
title = {{CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes}}, 
author = {Parks, Donovan H. and Imelfort, Michael and Skennerton, Connor T. and Hugenholtz, Philip and Tyson, Gene W.}, 
journal = {Genome Research}, 
issn = {1088-9051}, 
doi = {10.1101/gr.186072.114}, 
pmid = {25977477}, 
abstract = {{Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.}}, 
pages = {1043--1055}, 
number = {7}, 
volume = {25}, 
local-url = {file://localhost/Users/stephan/Documents/Papers%20Library/Parks/Parks_2015.pdf}
}

@ARTICLE{Chaumeil.2019,
  title    = "{GTDB-Tk}: a toolkit to classify genomes with the Genome Taxonomy
              Database",
  author   = "Chaumeil, Pierre-Alain and Mussig, Aaron J and Hugenholtz, Philip
              and Parks, Donovan H",
  abstract = "SUMMARY: The GTDB Toolkit (GTDB-Tk) provides objective taxonomic
              assignments for bacterial and archaeal genomes based on the
              Genome Taxonomy Database (GTDB). GTDB-Tk is computationally
              efficient and able to classify thousands of draft genomes in
              parallel. Here we demonstrate the accuracy of the GTDB-Tk
              taxonomic assignments by evaluating its performance on a
              phylogenetically diverse set of 10,156 bacterial and archaeal
              metagenome-assembled genomes. AVAILABILITY: GTDB-Tk is
              implemented in Python and licensed under the GNU General Public
              License v3.0. Source code and documentation are available at:
              https://github.com/ecogenomics/gtdbtk. SUPPLEMENTARY INFORMATION:
              Supplementary data are available at Bioinformatics online.",
  journal  = "Bioinformatics",
  month    =  nov,
  year     =  2019,
  language = "en"
}
@article{Raghunathan.2005,
  title={Genomic DNA amplification from a single bacterium},
  author={Raghunathan, Arumugham and Ferguson, Harley R and Bornarth, Carole J and Song, Wanmin and Driscoll, Mark and Lasken, Roger S},
  journal={Applied and environmental microbiology},
  volume={71},
  number={6},
  pages={3342--3347},
  year={2005},
  publisher={Am Soc Microbiol}
}
@ARTICLE{Rinke.2014,
  title    = "Obtaining genomes from uncultivated environmental microorganisms
              using {FACS-based} single-cell genomics",
  author   = "Rinke, Christian and Lee, Janey and Nath, Nandita and Goudeau,
              Danielle and Thompson, Brian and Poulton, Nicole and Dmitrieff,
              Elizabeth and Malmstrom, Rex and Stepanauskas, Ramunas and Woyke,
              Tanja",
  abstract = "Single-cell genomics is a powerful tool for exploring the genetic
              makeup of environmental microorganisms, the vast majority of
              which are difficult, if not impossible, to cultivate with current
              approaches. Here we present a comprehensive protocol for
              obtaining genomes from uncultivated environmental microbes via
              high-throughput single-cell isolation by FACS. The protocol
              encompasses the preservation and pretreatment of differing
              environmental samples, followed by the physical separation,
              lysis, whole-genome amplification and 16S rRNA-based
              identification of individual bacterial and archaeal cells. The
              described procedure can be performed with standard molecular
              biology equipment and a FACS machine. It takes <12 h of bench
              time over a 4-d time period, and it generates up to 1 $\mu$g of
              genomic DNA from an individual microbial cell, which is suitable
              for downstream applications such as PCR amplification and shotgun
              sequencing. The completeness of the recovered genomes varies,
              with an average of ∼50\%.",
  journal  = "Nat. Protoc.",
  volume   =  9,
  number   =  5,
  pages    = "1038--1048",
  month    =  may,
  year     =  2014,
  language = "en"
}
@ARTICLE{Quast.2013,
  title    = "The {SILVA} ribosomal {RNA} gene database project: improved data
              processing and web-based tools",
  author   = "Quast, Christian and Pruesse, Elmar and Yilmaz, Pelin and Gerken,
              Jan and Schweer, Timmy and Yarza, Pablo and Peplies, J{\"o}rg and
              Gl{\"o}ckner, Frank Oliver",
  abstract = "SILVA (from Latin silva, forest, http://www.arb-silva.de) is a
              comprehensive web resource for up to date, quality-controlled
              databases of aligned ribosomal RNA (rRNA) gene sequences from the
              Bacteria, Archaea and Eukaryota domains and supplementary online
              services. The referred database release 111 (July 2012) contains
              3 194 778 small subunit and 288 717 large subunit rRNA gene
              sequences. Since the initial description of the project,
              substantial new features have been introduced, including advanced
              quality control procedures, an improved rRNA gene aligner, online
              tools for probe and primer evaluation and optimized browsing,
              searching and downloading on the website. Furthermore, the
              extensively curated SILVA taxonomy and the new non-redundant
              SILVA datasets provide an ideal reference for high-throughput
              classification of data from next-generation sequencing
              approaches.",
  journal  = "Nucleic Acids Res.",
  volume   =  41,
  number   = "Database issue",
  pages    = "D590--6",
  month    =  jan,
  year     =  2013,
  language = "en"
}
@ARTICLE{Camacho.2009,
  title    = "{BLAST+}: architecture and applications",
  author   = "Camacho, Christiam and Coulouris, George and Avagyan, Vahram and
              Ma, Ning and Papadopoulos, Jason and Bealer, Kevin and Madden,
              Thomas L",
  abstract = "BACKGROUND: Sequence similarity searching is a very important
              bioinformatics task. While Basic Local Alignment Search Tool
              (BLAST) outperforms exact methods through its use of heuristics,
              the speed of the current BLAST software is suboptimal for very
              long queries or database sequences. There are also some
              shortcomings in the user-interface of the current command-line
              applications. RESULTS: We describe features and improvements of
              rewritten BLAST software and introduce new command-line
              applications. Long query sequences are broken into chunks for
              processing, in some cases leading to dramatically shorter run
              times. For long database sequences, it is possible to retrieve
              only the relevant parts of the sequence, reducing CPU time and
              memory usage for searches of short queries against databases of
              contigs or chromosomes. The program can now retrieve masking
              information for database sequences from the BLAST databases. A
              new modular software library can now access subject sequence data
              from arbitrary data sources. We introduce several new features,
              including strategy files that allow a user to save and reuse
              their favorite set of options. The strategy files can be uploaded
              to and downloaded from the NCBI BLAST web site. CONCLUSION: The
              new BLAST command-line applications, compared to the current
              BLAST tools, demonstrate substantial speed improvements for long
              queries as well as chromosome length database sequences. We have
              also improved the user interface of the command-line
              applications.",
  journal  = "BMC Bioinformatics",
  volume   =  10,
  pages    = "421",
  month    =  dec,
  year     =  2009,
  language = "en"
}
@ARTICLE{Tyson.2004,
  title    = "Community structure and metabolism through reconstruction of
              microbial genomes from the environment",
  author   = "Tyson, Gene W and Chapman, Jarrod and Hugenholtz, Philip and
              Allen, Eric E and Ram, Rachna J and Richardson, Paul M and
              Solovyev, Victor V and Rubin, Edward M and Rokhsar, Daniel S and
              Banfield, Jillian F",
  abstract = "Microbial communities are vital in the functioning of all
              ecosystems; however, most microorganisms are uncultivated, and
              their roles in natural systems are unclear. Here, using random
              shotgun sequencing of DNA from a natural acidophilic biofilm, we
              report reconstruction of near-complete genomes of Leptospirillum
              group II and Ferroplasma type II, and partial recovery of three
              other genomes. This was possible because the biofilm was
              dominated by a small number of species populations and the
              frequency of genomic rearrangements and gene insertions or
              deletions was relatively low. Because each sequence read came
              from a different individual, we could determine that
              single-nucleotide polymorphisms are the predominant form of
              heterogeneity at the strain level. The Leptospirillum group II
              genome had remarkably few nucleotide polymorphisms, despite the
              existence of low-abundance variants. The Ferroplasma type II
              genome seems to be a composite from three ancestral strains that
              have undergone homologous recombination to form a large
              population of mosaic genomes. Analysis of the gene complement for
              each organism revealed the pathways for carbon and nitrogen
              fixation and energy generation, and provided insights into
              survival strategies in an extreme environment.",
  journal  = "Nature",
  volume   =  428,
  number   =  6978,
  pages    = "37--43",
  month    =  mar,
  year     =  2004,
  language = "en"
}
@ARTICLE{Swan.2011,
  title    = "Potential for chemolithoautotrophy among ubiquitous bacteria
              lineages in the dark ocean",
  author   = "Swan, Brandon K and Martinez-Garcia, Manuel and Preston,
              Christina M and Sczyrba, Alexander and Woyke, Tanja and Lamy,
              Dominique and Reinthaler, Thomas and Poulton, Nicole J and
              Masland, E Dashiell P and Gomez, Monica Lluesma and Sieracki,
              Michael E and DeLong, Edward F and Herndl, Gerhard J and
              Stepanauskas, Ramunas",
  abstract = "Recent studies suggest that unidentified prokaryotes fix
              inorganic carbon at globally significant rates in the immense
              dark ocean. Using single-cell sorting and whole-genome
              amplification of prokaryotes from two subtropical gyres, we
              obtained genomic DNA from 738 cells representing most
              cosmopolitan lineages. Multiple cells of Deltaproteobacteria
              cluster SAR324, Gammaproteobacteria clusters ARCTIC96BD-19 and
              Agg47, and some Oceanospirillales from the lower mesopelagic
              contained ribulose-1,5-bisphosphate carboxylase-oxygenase and
              sulfur oxidation genes. These results corroborated community DNA
              and RNA profiling from diverse geographic regions. The SAR324
              genomes also suggested C(1) metabolism and a particle-associated
              life-style. Microautoradiography and fluorescence in situ
              hybridization confirmed bicarbonate uptake and particle
              association of SAR324 cells. Our study suggests potential
              chemolithoautotrophy in several uncultured Proteobacteria
              lineages that are ubiquitous in the dark oxygenated ocean and
              provides new perspective on carbon cycling in the ocean's largest
              habitat.",
  journal  = "Science",
  volume   =  333,
  number   =  6047,
  pages    = "1296--1300",
  month    =  sep,
  year     =  2011,
  language = "en"
}
@ARTICLE{Bankevich.2012,
  title    = "{SPAdes}: a new genome assembly algorithm and its applications to
              single-cell sequencing",
  author   = "Bankevich, Anton and Nurk, Sergey and Antipov, Dmitry and
              Gurevich, Alexey A and Dvorkin, Mikhail and Kulikov, Alexander S
              and Lesin, Valery M and Nikolenko, Sergey I and Pham, Son and
              Prjibelski, Andrey D and Pyshkin, Alexey V and Sirotkin,
              Alexander V and Vyahhi, Nikolay and Tesler, Glenn and Alekseyev,
              Max A and Pevzner, Pavel A",
  abstract = "The lion's share of bacteria in various environments cannot be
              cloned in the laboratory and thus cannot be sequenced using
              existing technologies. A major goal of single-cell genomics is to
              complement gene-centric metagenomic data with whole-genome
              assemblies of uncultivated organisms. Assembly of single-cell
              data is challenging because of highly non-uniform read coverage
              as well as elevated levels of sequencing errors and chimeric
              reads. We describe SPAdes, a new assembler for both single-cell
              and standard (multicell) assembly, and demonstrate that it
              improves on the recently released E+V-SC assembler (specialized
              for single-cell data) and on popular assemblers Velvet and
              SoapDeNovo (for multicell data). SPAdes generates single-cell
              assemblies, providing information about genomes of uncultivatable
              bacteria that vastly exceeds what may be obtained via traditional
              metagenomics studies. SPAdes is available online (
              http://bioinf.spbau.ru/spades ). It is distributed as open source
              software.",
  journal  = "J. Comput. Biol.",
  volume   =  19,
  number   =  5,
  pages    = "455--477",
  month    =  may,
  year     =  2012,
  language = "en"
}
@article{kang.2019,
  title={MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies},
  author={Kang, Dongwan D and Li, Feng and Kirton, Edward and Thomas, Ashleigh and Egan, Rob and An, Hong and Wang, Zhong},
  journal={PeerJ},
  volume={7},
  pages={e7359},
  year={2019},
  publisher={PeerJ Inc.}
}
@article{Wu.2014,
  title={MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm},
  author={Wu, Yu-Wei and Tang, Yung-Hsu and Tringe, Susannah G and Simmons, Blake A and Singer, Steven W},
  journal={Microbiome},
  volume={2},
  number={1},
  pages={1--18},
  year={2014},
  publisher={Springer}
}
@article{Wu.2016,
  title={MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets},
  author={Wu, Yu-Wei and Simmons, Blake A and Singer, Steven W},
  journal={Bioinformatics},
  volume={32},
  number={4},
  pages={605--607},
  year={2016},
  publisher={Oxford University Press}
}
@article{Criscuolo.2010,
  title    = "{BMGE} (Block Mapping and Gathering with Entropy): A new software
              for selection of phylogenetic informative regions from multiple
              sequence alignments",
  author   = "Criscuolo, Alexis and Gribaldo, Simonetta",
  abstract = "BACKGROUND The quality of multiple sequence alignments plays an
              important role in the accuracy of phylogenetic inference. It has
              been shown that removing ambiguously aligned regions, but also
              other sources of bias such as highly variable (saturated)
              characters, can improve the overall performance of many
              phylogenetic reconstruction methods. A current scientific trend
              is to build phylogenetic trees from a large number of sequence
              datasets (semi-)automatically extracted from numerous complete
              genomes. Because these approaches do not allow a precise manual
              curation of each dataset, there exists a real need for efficient
              bioinformatic tools dedicated to this alignment character
              trimming step. RESULTS Here is presented a new software, named
              BMGE (Block Mapping and Gathering with Entropy), that is designed
              to select regions in a multiple sequence alignment that are
              suited for phylogenetic inference. For each character, BMGE
              computes a score closely related to an entropy value. Calculation
              of these entropy-like scores is weighted with BLOSUM or PAM
              similarity matrices in order to distinguish among biologically
              expected and unexpected variability for each aligned character.
              Sets of contiguous characters with a score above a given
              threshold are considered as not suited for phylogenetic inference
              and then removed. Simulation analyses show that the character
              trimming performed by BMGE produces datasets leading to accurate
              trees, especially with alignments including distantly-related
              sequences. BMGE also implements trimming and recoding methods
              aimed at minimizing phylogeny reconstruction artefacts due to
              compositional heterogeneity. CONCLUSIONS BMGE is able to perform
              biologically relevant trimming on a multiple alignment of DNA,
              codon or amino acid sequences. Java source code and executable
              are freely available at
              ftp://ftp.pasteur.fr/pub/GenSoft/projects/BMGE/.",
  journal  = "BMC Evol. Biol.",
  volume   =  10,
  number   =  1,
  year     =  2010
}
@article{Oswald2017,
abstract = {Methane-oxidizing bacteria represent a major biological sink for methane and are thus Earth's natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was oxidized by filamentous gamma-proteobacteria related to Crenothrix polyspora. These filamentous bacteria have been known as contaminants of drinking water supplies since 1870, but their role in the environmental methane removal has remained unclear. While oxidizing methane, these organisms were assigned an 'unusual' methane monooxygenase (MMO), which was only distantly related to 'classical' MMO of gamma-proteobacterial methanotrophs. We now correct this assignment and show that Crenothrix encode a typical gamma-proteobacterial PmoA. Stable isotope labeling in combination swith single-cell imaging mass spectrometry revealed methane-dependent growth of the lacustrine Crenothrix with oxygen as well as under oxygen-deficient conditions. Crenothrix genomes encoded pathways for the respiration of oxygen as well as for the reduction of nitrate to N 2 O. The observed abundance and planktonic growth of Crenothrix suggest that these methanotrophs can act as a relevant biological sink for methane in stratified lakes and should be considered in the context of environmental removal of methane.},
author = {Oswald, Kirsten and Graf, Jon S. and Littmann, Sten and Tienken, Daniela and Brand, Andreas and Wehrli, Bernhard and Albertsen, Mads and Daims, Holger and Wagner, Michael and Kuypers, Marcel M.M. and Schubert, Carsten J. and Milucka, Jana},
doi = {10.1038/ismej.2017.77},
file = {:mnt/sdb/Scientific{\_}papers/ISME{\_}Oswald{\_}2017.pdf:pdf},
issn = {17517370},
journal = {ISME Journal},
number = {9},
pages = {2124--2140},
pmid = {28585934},
publisher = {Nature Publishing Group},
title = {{Crenothrix are major methane consumers in stratified lakes}},
url = {http://dx.doi.org/10.1038/ismej.2017.77},
volume = {11},
year = {2017}
}
@article{Hallam2006,
abstract = {Marine Crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. Prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic Crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. We report here analysis of fosmid sequences derived from the uncultivated marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction of carbon and energy metabolism. Genes predicted to encode multiple components of a modified 3-hydroxypropionate cycle of autotrophic carbon assimilation were identified, consistent with utilization of carbon dioxide as a carbon source. Additionally, genes predicted to encode a near complete oxidative tricarboxylic acid cycle were also identified, consistent with the consumption of organic carbon and in the production of intermediates for amino acid and cofactor biosynthesis. Therefore, C. symbiosum has the potential to function either as a strict autotroph, or as a mixotroph utilizing both carbon dioxide and organic material as carbon sources. From the standpoint of energy metabolism, genes predicted to encode ammonia monooxygenase subunits, ammonia permease, urease, and urea transporters were identified, consistent with the use of reduced nitrogen compounds as energy sources fueling autotrophic metabolism. Homologues of these genes, recovered from ocean waters worldwide, demonstrate the conservation and ubiquity of crenarchaeal pathways for carbon assimilation and ammonia oxidation. These findings further substantiate the likely global metabolic importance of Crenarchaeota with respect to key steps in the biogeochemical transformation of carbon and nitrogen in marine ecosystems.},
author = {Hallam, Steven J. and Mincer, Tracy J. and Schleper, Christa and Preston, Christina M. and Roberts, Katie and Richardson, Paul M. and DeLong, Edward F.},
doi = {10.1371/journal.pbio.0040095},
file = {:mnt/sdb/Scientific{\_}papers/PLoSBio{\_}Hallam{\_}2006.pdf:pdf},
issn = {1545-7885},
journal = {PLoS biology},
mendeley-groups = {Hydrocarbon Resource environments},
month = {apr},
number = {4},
pages = {e95},
pmid = {16533068},
title = {{Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16533068 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC1403158},
volume = {4},
year = {2006}
}
@article{Suzuki2012,
abstract = {Two novel ethylene-assimilating bacteria, strains ETY-M and ETY-NAG, were isolated from seawater around Japan. The characteristics of both strains were investigated, and phylogenetic analyses of their 16S rRNA gene sequences showed that they belonged to the genus Haliea. In C1-4 gaseous hydrocarbons, both strains grew only on ethylene, but degraded ethane, propylene, and propane in addition to ethylene. Methane, n-butane, and i-butane were not utilized or degraded by either strain. Soluble methane monooxygenase-type genes, which are ubiquitous in alkene-assimilating bacteria for initial oxidation of alkenes, were not detected in these strains, although genes similar to particulate methane monooxygenases (pMMO)/ammonia monooxygenases (AMO) were observed. The phylogenetic tree of the deduced amino acid sequences formed a new clade near the monooxygenases of ethane-assimilating bacteria similar to other clades of pMMOs in type I, type II, and Verrucomicrobia methanotrophs and AMOs in alpha and beta proteobacteria.},
author = {Suzuki, Toshihiro and Nakamura, Takamichi and Fuse, Hiroyuki},
doi = {10.1264/jsme2.ME11256},
file = {:mnt/sdb/Scientific{\_}papers/MicrobesEnviron{\_}Suzuki{\_}2012.pdf:pdf},
issn = {13426311},
journal = {Microbes and Environments},
keywords = {Haliea,Particulate methane monooxygenase (pmo),Short-chain alkene},
mendeley-groups = {thesis},
number = {1},
pages = {54--60},
pmid = {22307463},
title = {{Isolation of two novel marine ethylene-assimilating bacteria, Haliea species ETY-M and ETY-NAG, containing particulate methane monooxygenase-like genes}},
volume = {27},
year = {2012}
}
@article{Rochman2020,
abstract = {Copper-containing membrane monooxygenases (CuMMOs) are encoded by xmoCAB(D) gene clusters and catalyze the oxidation of methane, ammonia, or some short-chain alkanes and alkenes. In a metagenome constructed from an oilsands tailings pond we detected an xmoCABD gene cluster with {\textless}59{\%} derived protein sequence identity to genes from known bacteria. Stable isotope probing experiments combined with a specific xmoA qPCR assay demonstrated that the bacteria possessing these genes were incapable of methane assimilation, but did grow on ethane and propane. Single-cell amplified genomes (SAGs) from propane-enriched samples were screened with the specific PCR assay to identify bacteria possessing the target gene cluster. Multiple SAGs of Betaproteobacteria belonging to the genera Rhodoferax and Polaromonas possessed homologues of the metagenomic xmoCABD gene cluster. Unexpectedly, each of these two genera also possessed other xmoCABD paralogs, representing two additional lineages in phylogenetic analyses. Metabolic reconstructions from SAGs predicted that neither bacterium encoded enzymes with the potential to support catabolic methane or ammonia oxidation, but that both were capable of higher n-alkane degradation. The involvement of the encoded CuMMOs in alkane oxidation was further suggested by reverse transcription PCR analyses, which detected elevated transcription of the xmoA genes upon enrichment of water samples with propane as the sole energy source. Enrichments, isotope incorporation studies, genome reconstructions, and gene expression studies therefore all agreed that the unknown xmoCABD operons did not encode methane or ammonia monooxygenases, but rather n-alkane monooxygenases. This study broadens the known diversity of CuMMOs and identifies these enzymes in non-nitrifying Betaproteobacteria.},
annote = {- Show that the transcription of XmoA increases in the presence of propane, suggesting this gene is responsible for propane oxidation in Betaproteobacteria
-},
author = {Rochman, Fauziah F. and Kwon, Miye and Khadka, Roshan and Tamas, Ivica and Lopez-Jauregui, Azriel Abraham and Sheremet, Andriy and {V. Smirnova}, Angela and Malmstrom, Rex R. and Yoon, Sukhwan and Woyke, Tanja and Dunfield, Peter F. and Verbeke, Tobin J.},
doi = {10.1038/s41396-019-0561-2},
file = {:mnt/sdb/Scientific{\_}papers/ISME{\_}Rochman{\_}2020.pdf:pdf},
issn = {17517370},
journal = {ISME Journal},
mendeley-groups = {thesis},
number = {3},
pages = {714--726},
pmid = {31796935},
title = {{Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria}},
volume = {14},
year = {2020}
}