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.
2 answers
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.
Log in to answer this question.
-
merging of two assemblies from different short-reads techniques
written by Andrew Yu •
-
How do you split metagenomic bins/MAGs into eukaryotic and prokaryotic?
written by O.rka
-
How to search for similar sequences in all public metagenomes?
written by Dgg32
-
Use pre-assembled paired-end reads as single-end for metagenome assembly with metaSPAdes
written by somnja •
-
Necessary to filter out nanopore (or PacBio) reads before mapping?
written by BioinformaticsLad
-
Download summary tables from mg-Rast
written by djeppschmidt •
-
phase a non-model genome
written by devon.orourke •
-
De Novo Assembly of small RNA Reads (Illumina)
written by Seq225
-
categorising proteins into families when you have amino acid sequences
written by mwanerhi erfgtr •
-
Tutorial: Tools For Metagenomic Data Analysis
written by vijay
