Example: analyze a metagenome using 66,000 GTDB genomic representatives
sourmash-bio/sourmash-examples#14
This example uses the metagenome signature prepared in Example: create a metagenome signature from shotgun sequencing reads.
You'll also need to download the GTDB database as in Example: download and search 66,000 GTDB genomes with a query genome.
Now, run sourmash gather:
sourmash gather SRR5950647.sig gtdb-rs207.genomic-reps.dna.k31.zip
This should take about 5 minutes.
The output should look like this:
overlap p_query p_match avg_abund
--------- ------- ------- ---------
383.0 kbp 2.0% 7.8% 1.6 GCF_003697165.2 Escherichia coli DSM ...
187.0 kbp 1.0% 5.0% 1.6 GCF_015074785.1 Prevotella copri stra...
142.0 kbp 0.7% 2.8% 1.4 GCF_000012825.1 Bacteroides vulgatus ...
164.0 kbp 0.3% 1.4% 1.7 GCF_019127135.1 Prevotella copri stra...
found less than 50.0 kbp in common. => exiting
found 4 matches total;
the recovered matches hit 4.0% of the abundance-weighted query
This a minimum metagenome cover for the metagenome, based on the genomes in the GTDB database: in brief, it provides a shortest list of genomes that contain all of the known content in the metagenome (in this case, about 4%).
Note: more of the metagenome might be matched if you used a larger database or a database that included eukaryotic and/or host sequence.
Categories
This example belongs to the following categories: