Overlapping paired end reads in SOAPdenovo
Hi all!
I don't know if what I'm going to ask has ever been addressed (probably yes) or if I simply was not able to find any info regarding it but here is the question:
Is SOAPdenovo able to deal directly with overlapping paired end reads? And even if it does, does it make more sense to 1) use directly the overlapping PE reads or 2) merge the reads in longer single end reads and then use the resulting "extended" SE reads (plus the non-merged PE reads) to do the assembly? For instant, from what I read, with ABySS the 2nd strategy would be the one to use (no?).
Don't know if this matters for the 2nd part of the question but I'm about to receive Illumina HiSeq library of 100bp paired-end reads with insert size of 180bp.
Thanks in advance!
Fernando
I don't know if what I'm going to ask has ever been addressed (probably yes) or if I simply was not able to find any info regarding it but here is the question:
Is SOAPdenovo able to deal directly with overlapping paired end reads? And even if it does, does it make more sense to 1) use directly the overlapping PE reads or 2) merge the reads in longer single end reads and then use the resulting "extended" SE reads (plus the non-merged PE reads) to do the assembly? For instant, from what I read, with ABySS the 2nd strategy would be the one to use (no?).
Don't know if this matters for the 2nd part of the question but I'm about to receive Illumina HiSeq library of 100bp paired-end reads with insert size of 180bp.
Thanks in advance!
Fernando