Bwa-Mem And Quality Trimming

Question

[nupurgupta0806]

I want to switch from using bwa aln+sampe to bwa-mem, but I notice that there is no quality soft-trimming in the latter. (It is present in bwa aln). Am I missing something? Why has it not been included? Is there any other way to do this? Thanks!

Answer 1

[Istvan Albert]

you can use seqtk (also by Heng Li) to perform the trimming