fastp issue (trimming and read filtering tool)

Question

[v.berriosfarias]

Hello, has anyone used fastp? I used it for trimming metagenomic libraries , the issue is that I used as input a file with 40M sequences and the output was a file with 11M sequences.

the filtering results des not give detail of what happened with the removed sequences , although there is a report that details the removed reads given diverse filtering parameters (Q20, Q30, adapter trimming) but almost all the reads passes these filters (98% aprox).

So what do you think that happened with more of the half of the reads ?

https://www.dropbox.com/s/iefrzp62w0ap1f7/FPDEC2017_L1S1D05.html?dl=0

[GenoMax]

Perhaps you have adapter dimers (i.e. no inserts)? These would otherwise have good QC metrics (e.g Q scores).

People are not likely to click on Dropbox links. If you want to show extended data then perhaps use pastebin.com to post excerpts.

If you are willing to try an alternate tool out give bbduk.sh a try. A guide is available.