3.1 years ago by
Walnut Creek, USA
At least for Illumina reads, that's a bad idea. Especially for libraries under 140 bp, since you'd have nothing left (but assembly would run very fast!)
PacBio libraries don't have read-end adapters like Illumina. Rather, they have "Smart Bell" adapters somewhere in the middle of the read. PacBio's software already removes those for you when creating filtered subreads. Sometimes it doesn't get all of them, so I wrote a tool to remove them removesmartbell.sh), but it's not normally necessary. Therefore for PacBio my recommendation is: Do nothing, though you can try running removesmartbell.sh if you are feeling adventurous or are interested in knowing whether there are any leftover adapter sequences.
For Illumina, you should do adapter-trimming as indicated here. You can also use BBDuk to forcibly trim the first and last 70bp from every read, but I don't recommend that in this case.