Is the Abyss contig and scaffold phased?

Question

[wjar6718]

Hi,

Just wondering whether or not Abyss a contig or scaffold is phased into a particular strand of the DNA (although synthetic).

My guess would be 'Yes' because 1. The tool uses pair-end information 2. When I align scaffolds to human reference, hg19 and check via IGV (http://software.broadinstitute.org/software/igv/), I see many regions covering by 2 scaffolds, each of which has different orientations (forward or reverse), similar to pair-end reads or 2 DNA strands.

Thanks, James

Answer 1

[benv]

Hi James,

No, ABySS does not attempt to create a phased assembly. Like most de novo genome assemblers, it is a haploid assembler (it collapses heterozygous regions into a consensus).

W.r.t. to your contig alignments in IGV, it is normal to see pileups in repeat regions, but you generally should not see coverage > 1 in non-repeat regions, unless you are allowing your aligner to produce multiple alignments per contig and are not filtering out poor-quality alignments.