I've been trying to know more about pipelines for shotgun metagenomics data to use in my samples of water-borne bacteria, with a focus on rare cyanobacteria in particular.
Suggestions on what your favorite assemblers and functional annotation programs are most welcome!
Hello Angelo,
I have been working with megahit and metaSpades recently, they seem to do the job. For further binning of contigs I highly recommend anvi'o (http://merenlab.org/software/anvio/).
Hope that helps a bit!
Cheers
PS: for quick and dirty functional and taxonomic profiling of metagenomic data (unassembled), there's always MG-RAST
Hello Angelo,
I have been working with megahit and metaSpades recently, they seem to do the job. For further binning of contigs I highly recommend anvi'o (http://merenlab.org/software/anvio/).
Hope that helps a bit!
Cheers
PS: for quick and dirty functional and taxonomic profiling of metagenomic data (unassembled), there's always MG-RAST
Hi Igor,
Thanks for the suggestion! I am currently looking at megahit as well as it is quite popular. metaSPAdes should be also good since SPAdes worked well with my whole genome assemblies in the past. I'll look into it.
:)
Hello,
In addition the above excellent example, some vital "comparative insights" would be from here:
Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!: Article Comparing and Evaluating Metagenome Assembly Tools from a Mi...
Thanks,
Hi Biswapriya,
Thanks for the link! Great guide for metagenomics.
Cheers!
Hello. I use MOCAT2 by the Tara Oceans people.
http://mocat.embl.de/
It is currently installed in the Phil Genome Center Bioinfo server.
I find it user friendly.
Hello,
Another shotgun metagenomics pipelines that you can use are:
- EBI metagenomics (works like MG-Rast) https://www.ebi.ac.uk/metagenomics/
- Metamos
Article MetAMOS: A modular and open source metagenomic assembly and ...
- IMG/M
https://academic.oup.com/nar/article/42/D1/D568/1067396
-Ghostkoala
http://www.kegg.jp/ghostkoala/
- Clark
http://clark.cs.ucr.edu/
- Ghostx
Chapter GHOSTX: A Fast Sequence Homology Search Tool for Functional ...
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