The software for metagenomic DNA shotgun sequencing

[mot]

Hello,

I have metagenomic DNA shotgun sequencing data now. Are there any suggested software for analyzing ? Thank you for help.

[lorendarith]

Here's a good guide on what you can do with your data:

http://www.microbialinformaticsj.com/content/2/1/3

http://mmbr.asm.org/content/72/4/557.full

In short, you can try aligning your reads to known databases like Genbank (bacteria, virus and phage nucleotide and protein sequences). There are some recent fast tools to do so like Kraken and PAUDA. You can try assembling your reads into genomes with different assembly tools like Ray, MetaVelvet, IDBA, SOAPdenovo and then annotating the contigs. Or you can do some database independent analysis with differential coverage binning, clustering with machine learning algorithms and such.

[mot]

Thank you for suggestions. I got many contigs from my sequencing data. Are there any suitable tools for doing gene predicting for these contigs.

[nucacidhunter]

This paper and papers citing it might provide some ideas: http://genomebiology.com/2013/14/1/R2