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.