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Question: What is a HaploContig
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gravatar for afollette
5 weeks ago by
afollette • 0
afollette • 0 wrote:

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!
haplocontig • 77 views
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modified 5 weeks ago by lieven.sterck ♦ 10k • written 5 weeks ago by afollette • 0
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gravatar for lieven.sterck
5 weeks ago by
lieven.sterck ♦ 10k
VIB, Ghent, Belgium
lieven.sterck ♦ 10k wrote:

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)

ADD COMMENT • link written 5 weeks ago by lieven.sterck ♦ 10k
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