Example: create a metagenome signature from shotgun sequencing reads

sourmash-bio/sourmash-examples#12

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First, download two metagenome files:

curl -JLO ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR595/007/SRR5950647/SRR5950647_1.fastq.gz
curl -JLO ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR595/007/SRR5950647/SRR5950647_2.fastq.gz

This will create two 9.2MB files, SRR5950647_1.fastq.gz and SRR5950647_1.fastq.gz, containing shotgun metagenome reads from a stool sample (see ENA record).

Next, sketch the two metagenome files into a single signature:

sourmash sketch dna -p abund SRR5950647_?.fastq.gz -o SRR5950647.sig --name SRR5950647

This will produce a 150kb output file, SRR5950647.sig, containing a k-mer sketch built from both files.

You can see the details of the sketch with sourmash sig describe:

sourmash sig describe SRR5950647.sig

Categories

This example belongs to the following categories:

• introductory examples
• working with FASTQ files
• analyzing metagenomes