Best approach to analyze taxonomic profiling of metagenomes from environmental sample

[tigerxu]

I'm wondering which tool currently available is best for analyzing taxonomic profiling of environmental microbial community (non-human microbiome), e.g. soil, marine, sediment? I suppose that the analysis need to be done with all reads but not contigs.

Thanks in advance!

[rhinoceros]

I think mg-rast is a pretty great way to start..

[tigerxu]

Thank you rhinoceros!

I forgot a point. I hope to find a standalone software not web-based server. As MG-RAST or IMG is sometimes long waiting. I'm wondering if there is other fast and local approach. I knew MEGAN but searching NCBI NR is time-consuming.

[rhinoceros]

Thank you rhinoceros!

I forgot a point. I hope to find a standalone software not web-based server. As MG-RAST or IMG is sometimes long waiting. I'm wondering if there is other fast and local approach. I knew MEGAN but searching NCBI NR is time-consuming.

I don't know about IMG but I've sent dozens of samples to mg-rast and always gotten results within a few days. As to the speed of local approach, it depends on what kind of hardware you have, and of course, what you're doing. With a few hundred core server things can be done fast, not so with your average desktop. But consider e.g. the difference between working with raw reads and binned reads..

[tigerxu]

Sure, I will try MG-RAST. Thanks!