Question: CAP3: A DNA Sequence Assembly Program
0
gravatar for midox
5.8 years ago by
midox260
Tunisia
midox260 wrote:

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

 

thank you for your reply :)

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by midox260

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

ADD REPLYlink written 5.8 years ago by brentp23k

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

ADD REPLYlink written 5.8 years ago by midox260
1

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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 5.8 years ago by Chris Fields2.1k
1
gravatar for Chris Fields
5.8 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 5.8 years ago by Chris Fields2.1k
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