de novo assemble of metagenomics sequences

[biohumin]

Hi guys:
We now doing assemble metagenomics sequences which are from 454 GS FLX platform using Titanium Kit. There are 3 softwares (Newbler, Celera assembler and MIRA3) designed for 454 sequences. Is anyone has the experience use this softs? And how to set the best parameter for metagenome? How to confirm the accuracy of result owing to lack the reference genomes?

Thanks.

[sphil]

i am also interested in getting information about mira3 assembly with rna-seq data... so can anyone pls give a hint...

thx a lot

sphil

[colindaven]

You might be able to align against a reference genome / database with Blast etc, provided they exist.

Otherwise you can do
chimera checks
or genefinding

to check the accuracy of the contigs.

From what I have seen Newbler is the best assembler for 454, but I haven't compared the others.

[flxlex]

And if you do use newbler (or others), perhaps increase alignment stringency to try to prevent getting similar parts of the different genome assembled together, check out the -mi and -ml parameters (see also this post).

I've always wanted to try newblers cdna assembly option for metagenomes (just never got to it) because I think it could do a good job of assembling together those reads that come from the same part of the 'same' gene/genome in the samples... You would need to run clustering of the isotigs of each isogroup (e.g. by using cd-hit) afterwards, though...