Processing old Illumina v2 Mate Pair reads

[marcho]

Hi,

through a collaboration I got my hands on an old mate-pair dataset, generated in the pre Nextera days (MP kit v2, I am assuming). A "naive" mapping of these reads against a preliminary assembly shows that most reads are nowhere near the expected insert size of 5kb. So I was hoping to clean up the files to make sure that the reads are in fact properly trimmed/clipped and filtered. However, I have not been able to find much information how these reads are supposed to be processed, bioinformatically, so I can stuff them into e.g. Soap. Does anyone know of a tutorial/reference?

All the best,
Marc

[sklages]

You may want to try https://github.com/sequencing/NxTrim .. It is an Illumina tool for mp read processing.

[marcho]

Thanks - yes I was aware of NxTrim as well as Nextclip, both developed for Nextera MP libraries. Unfortunately, my libs are pre-Nextera, and it has been tricky to find out how these are to be processed.

[sklages]

oh, I missed the 'pre' :-)

So you probably should ask Illumina directly for their recommendation of processing such data.