Tools and parameters for reference assisted eukaryotic genome assembly using a draft genome as reference

Question

[WMJ]

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.

Answer 1

[colindaven]

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.