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CAP3: A DNA Sequence Assembly Program

Hello,

I wanted to know CAP 3 is an assembler reads Long or Short reads?

thank you for your reply :)

reads assembly-algorithms assembly
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updated by Ram Ram • written by midox midox

looks like Long reads to me as the example file has sequences > 900bp.

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written by brentp brentp

Thank you for your explanation.

Then? CAP3 treats Long reads?

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updated by Ram Ram • written by midox midox

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re: Cap3, I don't know but it will have problems with PacBio-like long reads (due to error rates). Moleculo is a possibility, I have seen people using it for transcriptome work back before better tools came along.

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updated by Ram Ram • written by Chris Fields Chris Fields

1 answer

It's a very simple OLC assembler if I recall; it may work for smaller assemblies but I don't know how it would handle reads of > 1000bp (it wsa developed for Sanger IIRC).

If you are using PacBio or Moleculo I suggest other assemblers, such as the latest Celera WGS release (which has support for both), possibly combined with minimus2 if you already have a short-read-based assembly. Also, I am testing out PBJelly2 w/ Moleculo data fpr the scaffolding/gap-filling with some success.

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updated by Ram Ram • written by Chris Fields Chris Fields

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