01. Home
Welcome to the MetScale wiki!
The workflows described in this wiki utilize snakemake to execute containerized tools for the analysis of paired-end Illumina sequences from metagenomes. The initial installation will create and activate your environment (see Install), and the offline setup will download all the files, databases, and biocontainers needed for operation on an air-gapped system (see Offline Setup). The documentation for each of the workflows is available in the order that they are intended to be run - read filtering, assembly, comparison, taxonomic classification, functional inference, and post processing. Within each workflow wiki page, you will learn how to prepare configuration ("config") files, which will specify your data, parameters, and rules to run offline.
The workflows described in this documentation have been tested with a set of paired-end Illumina reads from a subset of data described in Shakya et al. 20131. Subsequent pages of this wiki describe the example files and their results after running through each workflow. We highly encourage users to run through the workflows with the example dataset and parameters as specified in each of the workflow wiki pages before using new datasets and parameters.
Datasets Downloaded in the Offline Setup:
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SRR606249_subset10_1_reads_fq.gz(forward PE illumina reads)1 -
SRR606249_subset10_2_reads_fq.gz(reverse PE illumina reads)1 -
adapters_combined_256_unique.fasta(the adapter file)
These data sets represent a 10% subset of the full Shakya et al. 2013 dataset (SRR606249)1. For more information about the full dataset, please see the original publication:
1 Shakya, M., C. Quince, J. H. Campbell, Z. K. Yang, C. W. Schadt and M. Podar (2013). "Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities." Environ Microbiol 15(6): 1882-1899.
Please report issues as you work through the installation, setup, and workflows as described in this documentation. This is valuable feedback for our developers to receive, and we will respond to issues as soon as we can! Enjoy!