From 26cafa114989db7eb048b0371605e1cbbe19f997 Mon Sep 17 00:00:00 2001 From: Luiz Irber Date: Sat, 26 May 2018 04:22:35 -0700 Subject: [PATCH] Update dbs (#479) --- doc/databases.md | 28 ++++++++++++++++------------ 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/doc/databases.md b/doc/databases.md index 5dd629c64f..39e81a6af1 100644 --- a/doc/databases.md +++ b/doc/databases.md @@ -8,9 +8,9 @@ These database are formatted for use with `sourmash search` and Approximately 60,000 microbial genomes (including viral and fungal) from NCBI RefSeq. -* [RefSeq k=21, 2017.05.09][0] - 3.5 GB -* [RefSeq k=31, 2017.05.09][1] - 3.5 GB -* [RefSeq k=51, 2017.05.09][2] - 3.5 GB +* [RefSeq k=21, 2018.02.15][0] - 7 GB +* [RefSeq k=31, 2018.02.15][1] - 7 GB +* [RefSeq k=51, 2018.02.15][2] - 7.1 GB ## Genbank microbial genomes - SBT @@ -20,9 +20,9 @@ These database are formatted for use with `sourmash search` and Approximately 100,000 microbial genomes (including viral and fungal) from NCBI Genbank. -* [Genbank k=21, 2017.05.09][3]- 4.2 GB -* [Genbank k=31, 2017.05.09][4] - 4.2 GB -* [Genbank k=51, 2017.05.09][5] - 4.2 GB +* [Genbank k=21, 2018.02.15][3]- 8.4 GB +* [Genbank k=31, 2018.02.15][4] - 8.4 GB +* [Genbank k=51, 2018.02.15][5] - 8.4 GB ### Details @@ -43,12 +43,16 @@ sourmash compute -k 21,31,51 \ -o {output} \ {input} ``` -[0]:https://s3-us-west-1.amazonaws.com/spacegraphcats.ucdavis.edu/microbe-refseq-sbt-k21-2017.05.09.tar.gz -[1]:https://s3-us-west-1.amazonaws.com/spacegraphcats.ucdavis.edu/microbe-refseq-sbt-k31-2017.05.09.tar.gz -[2]:https://s3-us-west-1.amazonaws.com/spacegraphcats.ucdavis.edu/microbe-refseq-sbt-k51-2017.05.09.tar.gz -[3]:https://s3-us-west-1.amazonaws.com/spacegraphcats.ucdavis.edu/microbe-genbank-sbt-k21-2017.05.09.tar.gz -[4]:https://s3-us-west-1.amazonaws.com/spacegraphcats.ucdavis.edu/microbe-genbank-sbt-k31-2017.05.09.tar.gz -[5]:https://s3-us-west-1.amazonaws.com/spacegraphcats.ucdavis.edu/microbe-genbank-sbt-k51-2017.05.09.tar.gz + +See 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/refseq-d2-k21.tar.gz +[1]: https://s3-us-west-2.amazonaws.com/sourmash-databases/refseq-d2-k31.tar.gz +[2]: https://s3-us-west-2.amazonaws.com/sourmash-databases/refseq-d2-k51.tar.gz +[3]: https://s3-us-west-2.amazonaws.com/sourmash-databases/genbank-d2-k21.tar.gz +[4]: https://s3-us-west-2.amazonaws.com/sourmash-databases/genbank-d2-k31.tar.gz +[5]: https://s3-us-west-2.amazonaws.com/sourmash-databases/genbank-d2-k51.tar.gz ## Genbank LCA Database