Example: download, sketch, and search a collection of FASTA files

sourmash-bio/sourmash-examples#1

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Download 64 genomes from Awad et al., 2017:

curl -L https://osf.io/download/vbhy5 -o podar-ref.tar.gz
tar xzf podar-ref.tar.gz

Sketch them all in DNA space using default parameters, using GNU parallel per https://github.com/sourmash-bio/sourmash/issues/1796:

parallel -j 8 sourmash sketch dna {} -o {}.sig --name-from-first ::: $(ls *.fa)

Build a search database from all the signature files for k=31:

sourmash sig cat *.sig -k 31 -o podar-ref.zip

Search the database with one of the Shewanella genomes:

sourmash search 63.fa.sig podar-ref.zip

and you should see:

similarity   match
----------   -----
similarity   match
----------   -----
100.0%       NC_011663.1 Shewanella baltica OS223, complete genome
 32.1%       NC_009665.1 Shewanella baltica OS185, complete genome

Categories

This example belongs to the following categories:

• working with FASTA files
• examples using sourmash v4.x