What is a HaploContig

Question

[afollette]

Hey everyone,

I've been seeing the word haplocontig used when referencing de novo assembly pipelines. I believe I understand what a contig is, the combination of a group of reads that overlap without gaps. However, what nuance makes a normal contig a haplocontig?

Thanks!

Answer 1

[lieven.sterck]

from the top of my head: that would indicate a contig that is assigned to a specific haplotype. This is a somewhat new given, linked to the fact people are now doing haplotype aware assemblies (were back in the days we nearly all did consensus of haplotype assemblies) and where thus both haplotypes are being assembled as separate entities.

haplocontigs thus represent the same genomic region but from different haplotypes (you can see it a bit as allelic contigs)