How get sequences of specific bacteria from fastq metagenome using sourmash?

[marsfro]

Hello everyone!
I got taxonomy by sourmash gather, table with md5 hash numbers
How I could use it to extract specific reads (not contigs) of one Species (or Strain) from metagenome fastq file by sourmash?
Or might there are another ways?

Maria

[ctb]

hi @marsfro, please see the conversation here! #2535

The real answer is "map the reads to the genomes identified by sourmash", which you can do yourself or you can employ genome-grist to do.

I hope that helps!

[marsfro]

Thank you!

[ctb]

Added to #2184 in e828ff9:

How do I get the sequences for a particular reference genome from a metagenome, using sourmash?

If sourmash reports that a particular strain or genome is present in a
metagenome, how do you retrieve the reads using sourmash?

The short answer is: you have to use a different tool. You can do
read mapping between the metagenome and the relevant reference genome
(which can be automated with
the genome-grist workflow;
or, if you are interested in retrieving accessory elements, you can
try out
spacegraphcats.