Metagnomics assembly
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david martin
Feb 8, 2016, 9:28:51 PM2/8/16
to ABySS
Hi,
A very naive question . Is Abyss suitable for metagenomics assembly.
Right now i´m using megahit for contigs building and SOAPdenovo for scaffolding. Soapdenovo is not maintained anymore so i´m looking for other alternatives.
Has anybody tested in the context of metagenomics samples (human, soil...).
thanks for any update
david
A very naive question . Is Abyss suitable for metagenomics assembly.
Right now i´m using megahit for contigs building and SOAPdenovo for scaffolding. Soapdenovo is not maintained anymore so i´m looking for other alternatives.
Has anybody tested in the context of metagenomics samples (human, soil...).
thanks for any update
david
Alejandro Sanchez
Feb 8, 2016, 9:31:53 PM2/8/16
to david martin, ABySS
Hi David,
Normal genome assemblers are not suitable for metagenome assembly due to the different coverages that each organism will contribute to your dataset.
I recommend IDBA. Try it and good luck.
Cheers!
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