Fast whole-genome shotgun metagenomic tools

Question

[biotech]

We would like to set up a method for rapid pathogen detection in a diagnostics lab. Since assembly-dependent methods are time-costly, we are looking for tools to give metagenomics the possibility to serve as diagnostic method.

Thanks,
Bernardo

An example of these kind of tools is this one:

Koslicki, David, Simon Foucart, and Gail Rosen. "WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification." PloS one 9.3 (2014): e91784.

[JC]

Check Kraken

Answer 1

[Brian Bushnell]

I wrote a new tool, Seal, for this purpose. It's extremely fast, and assigns labels based on counting matching kmers to reference sequences. Seal is a derivative of BBDuk, with similar syntax:

seal.sh in=reads.fq ref=reference.fasta out=matched.fq rename stats=stats.txt rpkm=rpkm.txt

That will rename each read that matched something to indicate what it matched, and also output statstics of which sequences were present and how many reads matched them (in stats.txt), plus coverage and rpkms in (in rpkm.txt).

Answer 2

[Csaba Kerepesi]

We found Giant viruses in metagenomes from the Kutch Desert using a fast and simple method. You can follow this method to find pathogens against human metagenomes. We wrote the workflow in this article: Giant Viruses of the Kutch Desert

We are working on an automated version. I hope it helps.

Answer 3

[biotech]

Bioinformatics. 2014 Nov 10. pii: btu745. [Epub ahead of print]
Taxator-tk: Precise Taxonomic Assignment of Metagenomes by Fast Approximation of Evolutionary Neighborhoods.
Dröge J1, Gregor I1, McHardy AC2.