Question: Tools and parameters for reference assisted eukaryotic genome assembly using a draft genome as reference
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gravatar for WMJ
3.0 years ago by
WMJ10
WMJ10 wrote:

Hello!

I need to assemble a worm genome (Illumina Hiseq) using as reference a draft genome of the same species. What tool would be best for working on a 32 GB RAM workstation? And do I need any special parameters since the reference itself is a draft genome?

Thanks in advance.

ngs assembly • 926 views
ADD COMMENTlink modified 2.8 years ago by colindaven2.2k • written 3.0 years ago by WMJ10
0
gravatar for colindaven
2.8 years ago by
colindaven2.2k
Hannover Medical School
colindaven2.2k wrote:

You can have a look at the following on github. I used chromosomer with some success. I would first attempt an assembly vs C. elegans or another finished genome though. To be clear, with these programs you first need to do a de novo assembly, eg. with Abyss, soap-denovo etc

fenderglass / Ragout

Chromosome assembly using multiple references

gtamazian / chromosomer

A reference-assisted assembly tool for producing draft chromosome sequences.

ADD COMMENTlink written 2.8 years ago by colindaven2.2k
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