Detection of antibiotic resistance genes in shotgun metagenomic samples
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4.7 years ago

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 • 1.2k views
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have you tried ariba tool? or this tool

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

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

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

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4.7 years ago
gb ★ 2.2k

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

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

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

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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

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