Question: Long Runs Of A'S, G'S, C'S Or T'S In A Scaffolded Assembly (Abyss-1.3.4/Soapdenovo2)
gravatar for jomaco
6.8 years ago by
European Union
jomaco190 wrote:


As I understand, prior to scaffolding using long mate-pair reads, runs of N's or A/G/C/T's cannot exceed the length of the reads used for assembly (in this case 101bp). After scaffolding there are long series of N's as a result of contigs being joined together.

Can there also be long runs of A/G/C/T's after scaffolding? This is what I am seeing. I thought perhaps that joining contigs together ending in homopolymer repeats might, instead of an N, result in an A being used for example if those two contigs ended with long runs of A.

ABySS-1.3.4 was used for assembly and SOAPdenovo2 was used for scaffolding.



scaffolding • 1.5k views
ADD COMMENTlink modified 6.7 years ago by Rayan Chikhi1.4k • written 6.8 years ago by jomaco190
gravatar for Rayan Chikhi
6.7 years ago by
Rayan Chikhi1.4k
France, Lille, CNRS
Rayan Chikhi1.4k wrote:

Did you enable the gap-filling option during Soapdenovo2 scaffolding? I recall that Soapdenovo gapfiller does not hesitate to fill gaps with the same k-mer many times, to resolve tandem repeats.

ADD COMMENTlink written 6.7 years ago by Rayan Chikhi1.4k
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