flash for amplicons

[pooranis]

Out of curiousity, the description says:

Flash2 has some improvements from flash_1 including new logic from innie and outie overlaps as well as some initial steps for flash for amplicons

I saw the modifications for innies and outies in the readme, but what are the "initial steps for flash for amplicons"?

Thanks.

[msettles]

Basically, adapters dimers are relatively common in amplicons. flash2 uses a big dumb rule of if 50% of a read is low quality (I think <Q10 by default) it discards the read. Thats what that means

[pooranis]

Thanks for the reply! I'm working on a pre-processing pipeline for amplicon data for the Nephele project: https://nephele.niaid.nih.gov/
And I'm doing some testing to include FLASH2 as part of it, so that's why I was curious.