How should I use skewer to trim paired end reads?

Question

[jrleary]

I'm attempting to use skewer to trim paired end ChIPseq fastq files. I'm not solid on how to actually format the command used to run skewer as there's little in the way of user guides or documentation available. Here's what I'm using right now:

skewer -f auto -m pe -z -o ${sample}_trimmed.fastq.gz $read1 $read2

where $sample is the sample name, and $read1 and $read2 are the first and second paired end reads, respectively. This command only outputs one trimmed fastq file, and I believe it should output two, one for the first read and one for the second. Any tips would be greatly appreciated.

[GenoMax]

Are you open to using other trimming programs that have plenty of documentation? BBduk from BBMap suite, Trimmomatic or cutadapt.

[jrleary]

I like skewer because of fast it is, but I'm open to using other tools if the documentation / speed tradeoff is worth it

[GenoMax]

bbduk is plenty fast and is multi-threaded to boot. You can use multiple cores.

[Dave Carlson]

I'll second this suggestion and throw in an additional plug for fastp, which is also multi-threaded.

[jrleary]

I'll give both of these a look and compare their performance with that of skewer now that I've got it working. Thanks for the options.

Answer 1

[GenoMax]

As I see it, you need to provide a base name option (e.g. -o trimmed_files) to have trimmed files saved with that basename for skewer.

[jrleary]

This rectified the problem, thank you!