Question: Fast whole-genome shotgun metagenomic tools
0
gravatar for biotech
4.3 years ago by
biotech510
United States
biotech510 wrote:

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.

metagenomics • 1.2k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by biotech510

Check Kraken

ADD REPLYlink written 4.3 years ago by JC7.6k
0
gravatar for Brian Bushnell
4.3 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

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).

ADD COMMENTlink written 4.3 years ago by Brian Bushnell16k
0
gravatar for Csaba Kerepesi
4.3 years ago by
Hungary
Csaba Kerepesi320 wrote:

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.

ADD COMMENTlink written 4.3 years ago by Csaba Kerepesi320
0
gravatar for biotech
4.3 years ago by
biotech510
United States
biotech510 wrote:
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.
ADD COMMENTlink written 4.3 years ago by biotech510
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1495 users visited in the last hour