User: krsahlin

gravatar for krsahlin
krsahlin60
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Location:
State College
Website:
http://ksahlin.github.io/
Last seen:
3 years ago
Joined:
3 years, 6 months ago
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k*******@gmail.com

Posts by krsahlin

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Comment: C: Any advice for a de novo genome assembly
... Oh I missed that, my bad! It's likely that you are correct about bad indata. But just for the sake of further possible alternatives if OP decides to explore current data more: There are many genome projects of e.g., plants or fish, that are struggling with the contiguity of assemblies (N50 < 10 ...
written 3.0 years ago by krsahlin60
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Answer: A: Any advice for a de novo genome assembly
... As [Brian Bushnell](https://www.biostars.org/u/14684/) suggested, I would try Spades. The advantage of Spades to most other assemblers in this situation is the ability to handle “wide” k-mer distributions, such as the one you have. Although Spades assumes that the wide k-mer distribution is a result ...
written 3.0 years ago by krsahlin60
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Answer: A: N50 reduces after scaffolding
... This is most likely happening because SSPACE scaffolds together many of the smaller contigs. Furtheremore, (most of) the scaffolds created are smaller than original N50, i.e. less than 303kbp, ant most likely consists of only a pair, or a few contigs. The added N's into these smaller scaffolds infla ...
written 3.5 years ago by krsahlin60

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Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: N50 reduces after scaffolding

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