Question: How to identify SSR (Simple Sequence Repeats) for reference based assembly?
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gravatar for lakhujanivijay
3.7 years ago by
lakhujanivijay5.1k
India
lakhujanivijay5.1k wrote:

Can anybody suggest tools to identify SSRs for reference based assembly? Can MISA be used in that case?

ssr • 1000 views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by lakhujanivijay5.1k
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gravatar for Tonor
3.7 years ago by
Tonor420
UK
Tonor420 wrote:

RepeatAnalyzer: a tool for analysing and managing short-sequence repeat data https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2686-2

In the paper they mention Tandem Repeats Finder, scan_for_matches and the ALGGEN software suite.

ADD COMMENTlink written 3.7 years ago by Tonor420

So the point is:

  1. I have mapped HQ reads on my reference genome.
  2. Then I have called the consensus for the same.

My consensus sequence have 'N's. Before I can run any tool for SSR identification, shall I remove the 'N's (I guess yes).

OR

Shall I fill the gaps (N's) in the consensus sequence with any gap filler tool?

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by lakhujanivijay5.1k
0
gravatar for lakhujanivijay
3.7 years ago by
lakhujanivijay5.1k
India
lakhujanivijay5.1k wrote:

I realized that algorithms to identifying SSRs work on simple pattern matching; as simple as regex prgramming. Hence, it does not matter much when you know what fasta sequence are you supplying to your favourite SSR finding program. MISA will work as good as on consensus sequence as on assembled genome.

ADD COMMENTlink written 3.7 years ago by lakhujanivijay5.1k
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