Prepared search databases

RefSeq microbial genomes - SBT

These database are formatted for use with sourmash search and sourmash gather. They are calculated with a scaled value of 2000.

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

• RefSeq k=21, 2018.03.29 - 7 GB
• RefSeq k=31, 2018.03.29 - 7 GB
• RefSeq k=51, 2018.03.29 - 7.1 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, 2018.03.29- 8.4 GB
• Genbank k=31, 2018.03.29 - 8.4 GB
• Genbank k=51, 2018.03.29 - 8.4 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}

See github.com/dib-lab/sourmash_databases for a Snakemake workflow to build the databases.

Genbank LCA Database

These databases are formatted for use with sourmash lca; they are v2 LCA databases and will work with sourmash v2.0a11 and later. They are calculated with a scaled value of 10000 (1e5).

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

• Genbank k=21, 2017.11.07, 109 MB
• Genbank k=31, 2017.11.07, 120 MB
• Genbank k=51, 2017.11.07, 125 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.