Question: CAP3: A DNA Sequence Assembly Program
gravatar for midox
6.4 years ago by
midox260 wrote:

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


thank you for your reply :)

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by midox260

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

ADD REPLYlink written 6.4 years ago by brentp23k

thank you for your explanation. 
then? CAP3 treats Long reads?

ADD REPLYlink written 6.4 years ago by midox260

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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.

ADD REPLYlink written 6.3 years ago by Chris Fields2.1k
gravatar for Chris Fields
6.4 years ago by
Chris Fields2.1k
University of Illinois Urbana-Champaign
Chris Fields2.1k wrote:

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.

ADD COMMENTlink written 6.4 years ago by Chris Fields2.1k
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