I am currently trying to perform a new assembly using paired and mate paired reads. I first mapped my paired-end on a reference genome. Now I would like to extract from the mapping only the covered portions and get contigs from my reads (not a consensus with the reference genome including N between the uncovered portions). I would like then to use the paired-end reads and the mate paired to scaffold my assembly.
I there a proper way to do that ? I think maybe mpileup could help, but until now I only managed to produced consensus.
Extra question, which software would you recommend to perform the scaffolding ? Does any one exist allowing different insert size ?
Thank you very much!
Thanks a lot! I will try your method as soon as possible and let you know how it worked! It seems to do exactly what I want!
I'm almost done, however, I had this error at the second step:
Do I need the Verbose module, if yes, where could I find it ? I am not familiar with the those tools.
Verbose.pm comes with proovread, use
to make it visible to SeqFilter
Thanks! It is running!
How would this approach deal with indels?
They should look like in the reads, not like in the reference.