Can trimgalore be used to clean up mate pair libraries?

[gunjanpandey]

Wondering if trimgalore can be used to cleanup mate-paired libraries? Is yes, is there a specific flag(s)?

[FelixKrueger]

The standard use case would be single-end or paired-end reads. With mate-paired do you mean a special case of paired-end fragments with a (long) insert size? If so, I am afraid I don't know much about it (it's at least 10 years since I have heard this term...)

[gunjanpandey]

yes, I was wondering if mate-paired, a special case of paired-end fragments with a (long) insert size, could also be cleaned using trimgalore.

[FelixKrueger]

At the end of the day, it looks for a read-through adapter sequence (that typically results from fragments that are shorter than the read length), and trims off low quality base calls. If you think that either of these scenarios are applicable to your experimental setup - I don't see why it wouldn't work. But again, I don't have any experience with it I am afraid.