Question: Taxonomic assignments to metagenomic sequences
0
gravatar for jolespin
5.8 years ago by
jolespin130
United States
jolespin130 wrote:

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.  

ADD COMMENTlink modified 5.8 years ago by iraun3.8k • written 5.8 years ago by jolespin130
2
gravatar for iraun
5.8 years ago by
iraun3.8k
Norway
iraun3.8k wrote:

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.

ADD COMMENTlink modified 12 months ago by RamRS30k • written 5.8 years ago by iraun3.8k
1
gravatar for dago
5.8 years ago by
dago2.6k
Germany
dago2.6k wrote:

Maybe MEGAN is good for you

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by dago2.6k
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