Question: Detection of antibiotic resistance genes in shotgun metagenomic samples
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gravatar for BioinformaticsLad
29 days ago by
BioinformaticsLad140 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 • 139 views
ADD COMMENTlink modified 28 days ago by gb1.0k • written 29 days ago by BioinformaticsLad140
1

have you tried ariba tool? or this tool

ADD REPLYlink modified 29 days ago • written 29 days ago by hafiz.talhamalik140

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

ADD REPLYlink written 29 days ago by BioinformaticsLad140
1

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

ADD REPLYlink written 29 days ago by hafiz.talhamalik140
1
gravatar for gb
28 days ago by
gb1.0k
gb1.0k 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 28 days ago by gb1.0k

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

ADD REPLYlink written 28 days ago by BioinformaticsLad140
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 28 days ago by gb1.0k
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