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katerinakazantseva / strainy

Graph-based assembly phasing
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amplicon ONT sequencing of 740 known strains #85

Open weishwu opened 2 weeks ago

weishwu commented 2 weeks ago

Thanks for developing Strainy! I'm trying to use amplicon-based Nanopore reads to figure out strain abundances in bacterial samples. The pool has 740 strains and each sample may contain ~10 of them. I have the reference sequences of all these strains. I've been calculating the abundances based the alignments after stringent filtering to exclude potential sequencing errors. I'd like to try Strainy to see if I can get better results. Since I already have the strain references, I will use these sequences as the input to Strainy, but wonder whether Strainy has the resolution to distinguish two strains if they differ only at a couple of SNVs.

atabeerk commented 2 weeks ago

Hi @weishwu,

A couple of SNVs would be tricky for strainy. If they are close enough on the same unitig, strainy may be able to phase that unitig but if they are far apart, it would be more difficult.

If that doesn't work, you may try using one of the single strain references as the input.

weishwu commented 2 weeks ago

@atabeerk Thanks for your quick reply! My references are just ~1kb since this is amplicon sequencing, so I think it's promising.