Compatibility with reads showing a /1 /2 naming

[amanzanom]

Hello,

I am running into another weird error. I imagine it has to do with how polypolish reads the SAM files. Whenever I use Illumina sequences that use the /1 /2 ending for paired end sequencing, It seems polypolish crashes. This leaves me with having to do read file renaming, which I have to do for many many files (time and memory usage....). Not sure if this is a known issue or if it would be easy to fix, as it would be great.

Cheers

[rrwick]

Most of the data I work with has /1 and /2 suffixes, so Polypolish should work those read names. Are you using Bowtie2 instead of BWA-MEM? See this FAQ. If that isn't the problem, could you share the exact commands you ran and Polypolish's crash message? Thanks!