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0xTCG / biser

A fast tool for detecting and decomposing segmental duplications in genome assemblies
MIT License
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Does biser suitable for plant SD detection? #10

Closed Chenglin20170390 closed 2 years ago

Chenglin20170390 commented 2 years ago

Dear Ibrahim Numanagić,

Many thanks for develop such useful tool.

I wondering whether biser can detect SD for plant ?

I had try biser with my plant softmask genome, after overlap duplicate SD region, the segment duplication detected by biser account for about 30% of my totol plant genome.

I also try other software name asgart, it's report  about 3% SD of my totol genome.

I compared two softwares for detecting the bases of SD and SD excluded TE. I had draw a simple figure for better understand what I mean.
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inumanag commented 2 years ago

Hi @Chenglin20170390

Yes, it should be suitable for that. Note that BISER uses 75% similarity instead of 90% typically used by other tools, so it's expected to see more results in BISER's output.

Chenglin20170390 commented 2 years ago

Hi @inumanag ,

 Many thanks for you reply,  can we set the  parameter of biser similarity  to 90% ?  We would like to use it to  find the SD in plant genome.
 Thanks!
inumanag commented 2 years ago

Hi @Chenglin20170390

In v1.3, you can do that! Add --max-error=20 --max-edit-error=10. Also, adding --max_chromosome_size=100_000_000 might speed up the pipeline.