Taxonomic assignments to metagenomic sequences

Question

[jolespin]

So I have a metagenome file with multiple reads, created merged reads for higher quality, then assembled contigs using velvet.

Anyways, I want to figure out what organisms are in here. In the past, I've used MG-rast but there are some issues of them having the ability to put the data up publicly and it also takes a while to get the results. I found out about MGTAXA but my query has been running (on 5 MB file) for more than 2 days.

Are there any other tools I can use? Preferably tools with GUI but I can also use command line based programs if necessary.

Answer 1

[iraun]

I would suggest you to give a try to MetaCV. It classifies the reads instead of contigs into specific taxonomic and functional groups. Also MetaCV can generate really nice plots and tables automatically by an integrated R script. The output could also be visualized by MEGAN which has an user-friendly graphical interface.

• MetaCV tool
• MetaCV paper

Answer 2

[dago]

Maybe MEGAN is good for you