Published January 12, 2024 | Version 20240112
Dataset Open

ReferenceSeeker Database

Authors/Creators

  • 1. Justus Liebig University Giessen

Description

This repository provides pre-built databases for ReferenceSeeker (https://github.com/oschwengers/referenceseeker) comprising taxon specific databases for complete, reference and representative RefSeq genomes & plasmids as well as GTDB bacteria & archaea and PLSDB plasmids.

  • RefSeq (r221)
    • bacteria: 50,226
    • archaea: 905
    • fungi: 557
    • protozoa: 90
    • viruses: 14,012
  • GTDB (v214)
    • bacteria: 80,789 (not contained as it exceeds the standard storage quota - available upon request)
    • archaea: 4,416
  • plasmids
    • RefSeq: 81,674
    • PLSDB: 59,882

 

Files

Files (76.2 GB)

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md5:ea5fe6a1785fb28fc466f9a30ab4b08d
2.8 GB Download
md5:ae00de654a538a4138f02a25f46de4e8
897.0 MB Download
md5:61979a607532fbb589758e195e5b364a
59.6 GB Download
md5:ba220311adf2f11259f1203b4a5a3a99
5.9 GB Download
md5:e47b728d7f427d36793900c9b40b0cd4
2.3 GB Download
md5:ccbdb7e29c68e021fd1ea5aa73feb09b
2.6 GB Download
md5:10dda58b79989bc918d2e6d4be05c31f
1.1 GB Download
md5:9039d9c0e79574d1e6940e56d3a21ddd
1.0 GB Download

Additional details

Related works

Is referenced by
Software: https://github.com/oschwengers/referenceseeker (URL)

References

  • Schwengers et al., (2020). ReferenceSeeker: rapid determination of appropriate reference genomes. Journal of Open Source Software, 5(46), 1994, https://doi.org/10.21105/joss.01994