Question

CAP3: A DNA Sequence Assembly Program

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10.4 years ago

midox ▴ 290

Hello,

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

thank you for your reply :)

reads assembly-algorithms Assembly • 4.5k views

ADD COMMENT • link updated 3.1 years ago by Ram 44k • written 10.4 years ago by midox ▴ 290

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

ADD REPLY • link 10.4 years ago by brentp 24k

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Thank you for your explanation.

Then? CAP3 treats Long reads?

ADD REPLY • link updated 3.1 years ago by Ram 44k • written 10.4 years ago by midox ▴ 290

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If you aren't answering your own question and intend on leaving a comment, you should click the 'Add Comment' underneath the answer or comment you are addressing.

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.

ADD REPLY • link updated 3.1 years ago by Ram 44k • written 10.4 years ago by Chris Fields ★ 2.2k

Ram · Answer 1 · 2014-06-19

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.