bfast with illumina mate-pair and insert size estimation

[Protaeus]

Do reads from the illumina mate-pair need to be reverse-complemented prior to alignment?

On a somewhat unrelated note, I have noted that the insert size estimation from bfast is not anywhere near what I would expect. I am not using ungapped pairing nor am I providing a std dev for insert size. Is this expected? If not, do you have a guess as to why this may be the case? When I run the same data in bwa (or assemble with velvet), the estimated insert size if right-on, so I don't think it's a library issue.

[nilshomer]

Do reads from the illumina mate-pair need to be reverse-complemented prior to alignment?

No

On a somewhat unrelated note, I have noted that the insert size estimation from bfast is not anywhere near what I would expect. I am not using ungapped pairing nor am I providing a std dev for insert size. Is this expected? If not, do you have a guess as to why this may be the case? When I run the same data in bwa (or assemble with velvet), the estimated insert size if right-on, so I don't think it's a library issue.

Send an example to [email protected]

[shanebrubaker]

Response to reverse complement question

I'm not sure if anyone ever answered this. Yes reads from Illumina Mate Pair (long-insert) libraries should be reverse-complemented for velvet. Other assemblers might be different.

[Protaeus]

I'm not sure if anyone ever answered this. Yes reads from Illumina Mate Pair (long-insert) libraries should be reverse-complemented for velvet. Other assemblers might be different.

Thanks for getting back to me. I eventually figured it out through trial and error!