Assembly-free metagenomics tools

Question

[biotech]

We would like to set up a bioinformatic method to analyse high throughput metagenomics data avoiding the assembly step. Our objective is to get taxonomy and functional information of metagenomics samples.

I open this thread for people to post this kind of tools.

Thanks,

Although some papers have been published, seems this strategy is under development:

Luo, Haiwei, and Mary Ann Moran. "Assembly‐free metagenomic analysis reveals new metabolic capabilities in surface ocean bacterioplankton."Environmental microbiology reports 5.5 (2013): 686-696.

Sunagawa, Shinichi, et al. "Metagenomic species profiling using universal phylogenetic marker genes." Nature methods 10.12 (2013): 1196-1199.

Answer 1

[5heikki]

MG-RAST does everything for you. Keep in mind though that taxonomic and functional assignments from short reads come with low statistical support..

Answer 2

[Juke34]

You should also look "Kraken"

Answer 3

[Csaba Kerepesi]

AmporaNet and AmphoraVizu are simple and great online tools for analysis of assembly-free shotgun sequenced metagenomic data.