databases.md

Prepared search databases

RefSeq microbial genomes - SBT

These database are formatted for use with sourmash search and sourmash gather.

Approximately 60,000 microbial genomes (including viral and fungal) from NCBI RefSeq.

• RefSeq k=21, 2017.05.09 - 3.5 GB
• RefSeq k=31, 2017.05.09 - 3.5 GB
• RefSeq k=51, 2017.05.09 - 3.5 GB

Genbank microbial genomes - SBT

These database are formatted for use with sourmash search and sourmash gather.

Approximately 100,000 microbial genomes (including viral and fungal) from NCBI Genbank.

• Genbank k=21, 2017.05.09- 4.2 GB
• Genbank k=31, 2017.05.09 - 4.2 GB
• Genbank k=51, 2017.05.09 - 4.2 GB

Details

The individual signatures for the above SBTs were calculated as follows:

sourmash compute -k 4,5 \
                         -n 2000 \
                         --track-abundance \
                         --name-from-first \
                         -o {output} \
                         {input}

sourmash compute -k 21,31,51 \
                         --scaled 2000 \
                         --track-abundance \
                         --name-from-first \
                         -o {output} \
                         {input}

Genbank LCA Database

These databases are formatted for use with sourmash lca.

Approximately 87,000 microbial genomes (including viral and fungal) from NCBI Genbank.

• Genbank k=21, 2017.11.07, 105 MB
• Genbank k=31, 2017.11.07, 118 MB
• Genbank k=51, 2017.11.07, 123 MB

Details

The above LCA databases were calculated as follows:

sourmash lca index genbank-genomes-taxonomy.2017.05.29.csv \
    genbank-k21.lca.json.gz -k 21 --scaled=10000 \
    -f --traverse-directory .sbt.genbank-k21 --split-identifiers

See github.com/dib-lab/2018-ncbi-lineages for information on preparing the genbank-genomes-taxonomy file.