Pathway analysis from MGRAST output

Question

[ARich]

Hi Biostar community,

I am interested to know if there is a tool or software which can take mgrast pathway output and provide list of altered pathways between the groups. and provide nice visualization with good resolution.

Thanks!

Answer 1

[natasha.sernova]

See these sites:

ftp://ftp.metagenomics.anl.gov/data/manual/mg-rast-manual.pdf

it's a paper from 2011, but it is highly cited:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044276/

This paper is from 2012 and also highly cited.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038183

It's very recent and has nice visualization:

http://www.bioconductor.org/packages/release/bioc/vignettes/mmnet/inst/doc/mmnet.pdf

There is ngs-tools discussion as well:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3794082/