Open ctb opened 1 year ago
Added to #2184 in 69dfbc08:
Yes! (And see the FAQ above, How do k-mer analyses compare with read mapping?
If you're interested in picking a single best reference genome (from a large database) for read mapping, you can do the following:
sourmash sketch dna
, and/or download
one of our prepared databases. You can use default parameters for sourmash sketch
.sourmash sketch dna
.sourmash prefetch reads.sig <reference genome sketch collection(s)> -o matches.csv
matches.csv
on the f_match_query
column and pick the highest value -
this is the k-mer detection - and pick the match name from the match_name
column;If you want to map a metagenome to multiple references, consider
using sourmash gather
and/or
the genome-grist workflow.
(This is also known as "read recruitment.")
This came up on microbial bioinformatics slack, thought I'd share - topic was selecting from many viral genomes.