Question: Detection of antibiotic resistance genes in shotgun metagenomic samples
0
gravatar for BioinformaticsLad
9 months ago by
BioinformaticsLad160 wrote:

There are several pipelines for detection of ARGs using assembled contigs but I was wondering if anyone has had any luck performing ARG detection using raw reads? There's GROOT, which is quite new, so I'm not sure performance.

metagenomics • 303 views
ADD COMMENTlink modified 9 months ago by gb1.8k • written 9 months ago by BioinformaticsLad160
1

have you tried ariba tool? or this tool

ADD REPLYlink modified 9 months ago • written 9 months ago by hafiz.talhamalik230

I know baout Ariba but the analysis requires assembly. fARGene I don't know about - I'll check it out, thanks!

ADD REPLYlink written 9 months ago by BioinformaticsLad160
1

as per their methodology they are simply converting fastq reads into Fasta using seqtk and then continuing with fasta reads.

ADD REPLYlink written 9 months ago by hafiz.talhamalik230

I looked in Ariba more and the authors say it's not suitable for metagenomic samples

ADD REPLYlink written 8 months ago by BioinformaticsLad160
1
gravatar for gb
9 months ago by
gb1.8k
gb1.8k wrote:

raw reads... Just BLAST? https://card.mcmaster.ca/

If it are to much reads you could dereplicate first or/and set some quality tresholds.

ADD COMMENTlink written 9 months ago by gb1.8k

I thought about that, but it would take an inordinate amount of time. Each of my samples is 30Gbp!

ADD REPLYlink written 9 months ago by BioinformaticsLad160
1

yes that is true but it depends a lot on your reference database. Blasting against genbank is impossible these days with that amount of reads. So a few options that I can think of:

Or let go the raw reads part and do an assembly and gene prediction

ADD REPLYlink written 9 months ago by gb1.8k
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: 782 users visited in the last hour