Scaffolding tools for metagenomics ???

[danova]

Hello,
I´m currently working on paired end data (2*150) to build a metagenomics assembly.

So far i´m using the combination of megahit to build contigs and soapdenovo for scaffolding. soapdenovo is not mainained anymore.

Does anybody worked with other scaffolding tools ??? SSpace seem to do the job but it´s not opensource.

thanks for sharing your experience.

david

[fibar]

Hi,
We've been using Velvet-MetaVelvet for a same type of data set, and we are pretty happy with it.
Check steps at http://metavelvet.dna.bio.keio.ac.jp/
Cheers!

[Markiyan]

You can give Newbler a try, but proper matepair would be essential for good res...

Dear David,

Newbler assembler (v3 or v2.8) actually has quite good scaffolding module, provided you give it good and properly preprocessed (cleaned) data in the fastq format...

Also any tool is limited to the range of the input data (max. 1.2kb for illumina shotgun),
So a proper matepair (or 454 PE is a must, if yours repeats are longer than 900bp.

See bellow for more info:
http://seqanswers.com/forums/showthread.php?t=62617

Markiyan.

Hello,
Does anybody worked with other scaffolding tools ??? SSpace seem to do the job but it´s not opensource.

david

[bastianwur]

Opera also scaffolds.

It might be recommendable to first to binning on the contigs and afterwards the scaffolding, because it might lead to better results (due to less ambiguous mapping within the bins)