Prepared search databases¶
RefSeq microbial genomes¶
These database are formatted for use with sourmash sbt_search
and
sourmash sbt_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¶
These database are formatted for use with sourmash sbt_search
and
sourmash sbt_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}