microbe-dbs

Utilities to fetch biological databases relevant for microbial genomics analysis.

Some database require python to download and at least 2 libraries (biopython and requests).

You can install the environment with conda from the environment.yml file.

conda env create -f environment.yml
conda activate microbe-dbs

Use the bash CLI to list databases.

./microbe-dbs -h
 microbe-dbs <databases> <output>
    
    databases :
      -> uniprotkb_bacteria
      -> refseq_bacteria
      -> refseq_plasmid
      -> refseq_viral
      -> ncbi_arg
      -> vfdb
      -> ...

Databases

Bacteria

uniprotkb_bacteria

• description: UniprotKB (SwissProt/TrEMBL) - Bacteria
• release: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/reldate.txt
• url: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/
• license: Creative Commons Attribution (CC BY 4.0)

refseq_bacteria

• description: RefSeq: NCBI Reference Sequence Database
• release: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER
• url: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/bacteria/
• license: NCBI places no restrictions on the use or distribution. However, submitters may claim copyright of the data they have submitted.

refseq_plasmid

• description: RefSeq: NCBI Reference Sequence Database
• release: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER
• url: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/
• license: NCBI places no restrictions on the use or distribution. However, submitters may claim copyright of the data they have submitted.

cog

• description: Clusters of Orthologous Groups of proteins database
• release: 2014 update
• url: https://www.ncbi.nlm.nih.gov/COG/
• license: NCBI places no restrictions on the use or distribution. However, submitters may claim copyright of the data they have submitted.

pub_mlst

• description: PubMLST - Public databases for molecular typing and microbial genome diversity.
• release: by date (https://pubmlst.org/news.shtml)
• url: https://pubmlst.org/
• license: https://pubmlst.org/policy.shtml [7]

vfdb

• description: Virulence Factor Database
• release: by date
• url: http://www.mgc.ac.cn/VFs/download.htm
• license: none reported. Copyrighted to Key Laboratory of Systems Biology of Pathogens, Institue of Pathogen Biology, CAMS&PUMC, Bejing, China.

isfinder

• description: ISFinder Database
• release: by date
• url: https://github.com/thanhleviet/ISfinder-sequences
• license: none reported. Citation needed.

mibig

• description: The Minimum Information about a Biosynthetic Gene cluster (MIBiG) database
• release: Version 1.4 (August 6th, 2018)
• url: http://mibig.secondarymetabolites.org
• license: Creative Commons Attribution 4.0 International License

bacdive

• description: The Bacterial Diversity Metadatabase
• release: by date
• url: https://www.bacdive.de/
• license: See Term of use and Copyright (https://bacdive.dsmz.de/about)

resfinder_db

• description: ResFinder DB - ResFinder identifies acquired antimicrobial resistance genes and/or chromosomal mutations
• release: last git commit date
• url: https://bitbucket.org/genomicepidemiology/resfinder_db/
• license: Apache License, Version 2.0 (the "License")

ncbi_arg

• description: NCBI - Bacterial Antimicrobial Resistance Reference Gene Database
• release: by date
• url: https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/Data/
• license: Public Domain (see https://raw.githubusercontent.com/ncbi/amr/master/LICENSE)

ebi_mgnify_hg

• description: EBI MGnify Human Gut Proteins Catalogue 90 (high quality)
• release: by date
• url: http://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/2019_09/uhgp_catalogue/uhgp-90/
• license: See https://www.ebi.ac.uk/metagenomics/about

Virus

refseq_viral

• description: RefSeq: NCBI Reference Sequence Database
• release: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER
• url: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/
• license: NCBI places no restrictions on the use or distribution. However, submitters may claim copyright of the data they have submitted.

Other

ncbi_taxonomy

• description: NCBI Taxonomy
• release: by date
• url: ftp://ftp.ncbi.nih.gov/pub/taxonomy/
• license: NCBI places no restrictions on the use or distribution. However, submitters may claim copyright of the data they have submitted.

refseq_archaea

• description: RefSeq: NCBI Reference Sequence Database
• release: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER
• url: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/archaea/
• license: NCBI places no restrictions on the use or distribution. However, submitters may claim copyright of the data they have submitted.

refseq_fungi

• description: RefSeq: NCBI Reference Sequence Database
• release: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER
• url: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/fungi/
• license: NCBI places no restrictions on the use or distribution. However, submitters may claim copyright of the data they have submitted.

ebi_idmapping

• description: EBI - Uniprot ID mappings with different databases
• release: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/RELEASE.metalink
• url: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/
• license: Creative Commons Attribution-NoDerivs 3.0