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v22.09: Pyu Ancient Cities
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@jfy133 jfy133 released this 30 Aug 10:59
· 1300 commits to master since this release
v22.09
d14b0d8

Sixth (and long-awaited) major release of AncientMetagenomeDir.

This release includes a significant update to the repository, with an extension to DNA sequencing library level metadata! You can now use these tables to directly download sequencing data, with knowledge of their construction to help with informed processing of public data. The release also sees the deprecation of the 'Anthropgenic' metagenome table due to a lack of interest. This will be reinstated in the future if of interest to the community.

Release v22.09 includes 6 new publications and 3 removed publications, representing 23 new ancient host-associated metagenome samples, 165 new ancient microbial genomes, and 7 new (previously missed) ancient environmental samples.

It adds 1829 new ancient host-associated metagenome libraries, 2096 new ancient microbial genome libraries, and 440 new ancient environmental libraries.

This brings the repository to a total of 126 publications, 1061 new ancient host-associated metagenome samples, 533 ancient microbial genomes, and 382 new ancient environmental samples. It also includes 1829 new ancient host-associated metagenome libraries, 2096 new ancient microbial genome libraries, and 440 new ancient environmental libraries.

Corrections were made to 29 publications.

New Contributors

CHANGELOG

Added

  • Extended repository to include library level metadata for all existing samples

Ancient Metagenome: Host Associated

  • Granehäll 2021 10.1186/s40168-021-01132-8
  • Maixner 2021 10.1016/j.cub.2021.09.031
  • Kazarina 2021b 10.1016/j.jasrep.2021.103213

Ancient Single Genome: Host Associated

  • Granehäll 2021 10.1186/s40168-021-01132-8
  • Pfrengle 2021 10.1186/s12915-021-01120-2
  • Kocher 2021 10.1126/science.abi5658
  • Andrades Valtueña 2022 10.1073/pnas.2116722119

Ancient Metagenome: Environmental

Ancient Metagenome: Anthropogenic

  • Due to the lack of community interest, this table has now been deprecated and will not be included in future releases of AncientMetagenomeDir. However it will be reinstated in the future if interest returns.

Misc

  • Added library metadata for FASTQ and BAM level data
  • Changed the missing value from NA to Unknown for archive_project for the samples tsv
  • Removed 'sampling date' columns from host-associated metagenome and single-genome sample tables as this is almost never reported

Changed

  • Changed archive_project from NA to Unknown for Taubenberger2005, PattersonRoss2018, Worobey2016
  • Fixed Susat2021 DOIs (excel dragging error)
  • Fixed Kazarina2021 Project/Sample accessions (column flip error)
  • Fixed Morozova2020 DOIs (excel dragging error)
  • Fixed Bieker2020 DOIs (paper partly reused previous data for new purpose and earlier had the other publication DOI. Now made all DOIs and dates consistent for the publication where metagenomics was performed)
  • Fixed Bieker2020 sample USNH-39 into two separate 'artifical samples' due to upload of two libraries to two difference archives.
  • Fixed Bieker2020 missing sample accession codes (due to later re-sequencing and non-reused SRS/ERS code)
  • Fixed Muhlemann2018 Project ID (now available)
  • Fixed FellowsYates2021 corrected typo in longitude 85.53 > -85.53
  • Fixed Velsko2018 project name to Velsko2019 (wrong publication year)
  • Fixed Schuenemann2011 Put the accession ID of the full plasmid sequence not partial
  • Fixed Martin2013 corrected archive name (incorrectly reported in publication)
  • Fixed Seersholm2016 archive ENA (from incorrectly specified as SRA)
  • Fixed Eisenhofer2020 date rounding error (originally added 230 rather than 200)
  • Fixed BravoLopez2020 typo in site name (Inmaculate -> Immaculate)
  • Fixed Willmann2018 project_name (originally missing the second 'n')
  • Fixed DeDios2020, DeDios2019, DeDios2021 project_names (originally had lowercase leading d)
  • Fixed DeDios2020 sample_name from Jean-Paul Marat to Marat to make it consistent with the libraries uploaded in the ENA
  • Fixed Campos2021 sample accession column had run accession
  • Fixed Philips2017 fixed incorrect DOI (from later publication that reused same data)
  • Fixed Wagner2014 incorrect archive in the samples tsv
  • Fixed Eerkens2018 sample name from an individual name to the specific calculus sample name
  • Fixed Zhou2018 by switching sample name to a clearer one based on the file name rather than just the project_archive ID
  • Fixed Zhou2018 in ancientsinglegenome-hostassociated archive_project and archive_accession to be more explicit as of which files have been use to reconstruct the genome
  • Fixed Campos2021 sample_name to HERB_1937 to make it consistent with the libraries uploaded in the ENA
  • Fixed Borry2020 sample_name to match archaeological ID from paper (as opposed to laboratory ID which was in sample.tsv table)
  • Fixed Velsko2019 accidental inclusion of old sample accessions to keep 'correct' sample accession of correct data
  • Fixed Liang2021 sample names to be more specific to allow association with library names
  • Fixed GuzmanSolis2021 archive_project and archive_accession to include the Dryad doi and the specific ids from the download links
  • Fixed Ardelean2020 sample_name incorrect in samples tsv, replaced with sample_name from libraries tsv
  • Fixed Morozova2020 typo in - Azov37 -> Axov38
  • Fixed Morozova2020 accidental ERS code duplication across two samples

Removed

  • Removed Mendum2014 sample SK27 due to TreeBASE repository not being accessible any more
  • Removed SantiagoRodriguez2016 and SantiagoRodridguez2016 samples as raw data is no longer publicly accessible on MG-RAST
  • Removed Braadbaart2020 as uploaded data was not shotgun data as required for inclusion in environmental table
  • Removed Worobey2016 samples SF74 and SF73 as not in final consensus sequences
  • Removed Schulte2021 sample accessions of targeted capture libraries (which were different from the shotgun libraries)
  • Removed Schuenemann2018 libraries (Jørgen_*) that were originally published in tandem with and already included in KrauseKyora2018b

Pyu Ancient Cities

Pyu Ancient Cities includes the remains of three brick, walled and moated cities of Halin, Beikthano and Sri Ksetra located in vast irrigated landscapes in the dry zone of the Ayeyarwady (Irrawaddy) River basin. They reflect the Pyu Kingdoms that flourished for over 1,000 years between 200 BC and AD 900. The three cities are partly excavated archaeological sites. Remains include excavated palace citadels, burial grounds and manufacture sites, as well as monumental brick Buddhist stupas, partly standing walls and water management features – some still in use – that underpinned the organized intensive agriculture.

Description used under license CC-BY-SA IGO 3.0

Contributors

Xevkin, ossmith, and 21 other contributors
Assets 3
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