# 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][0] - 7 GB * [RefSeq k=31, 2018.03.29][1] - 7 GB * [RefSeq k=51, 2018.03.29][2] - 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][3]- 8.4 GB * [Genbank k=31, 2018.03.29][4] - 8.4 GB * [Genbank k=51, 2018.03.29][5] - 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](https://github.com/dib-lab/sourmash_databases) for a Snakemake workflow to build the databases. [0]: https://s3-us-west-2.amazonaws.com/sourmash-databases/2018-03-29/refseq-d2-k21.tar.gz [1]: https://s3-us-west-2.amazonaws.com/sourmash-databases/2018-03-29/refseq-d2-k31.tar.gz [2]: https://s3-us-west-2.amazonaws.com/sourmash-databases/2018-03-29/refseq-d2-k51.tar.gz [3]: https://s3-us-west-2.amazonaws.com/sourmash-databases/2018-03-29/genbank-d2-k21.tar.gz [4]: https://s3-us-west-2.amazonaws.com/sourmash-databases/2018-03-29/genbank-d2-k31.tar.gz [5]: https://s3-us-west-2.amazonaws.com/sourmash-databases/2018-03-29/genbank-d2-k51.tar.gz ## 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](https://osf.io/d7rv8/download), 109 MB * [Genbank k=31, 2017.11.07](https://osf.io/4f8n3/download), 120 MB * [Genbank k=51, 2017.11.07](https://osf.io/nemkw/download), 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](https://github.com/dib-lab/2018-ncbi-lineages) for information on preparing the genbank-genomes-taxonomy file.