Detection of antibiotic resistance genes in shotgun metagenomic samples

Question

[BioinformaticsLad]

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.

[hafiz.talhamalik]

have you tried ariba tool? or this tool

[BioinformaticsLad]

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

[hafiz.talhamalik]

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

[BioinformaticsLad]

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

Answer 1

[gb]

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

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

[BioinformaticsLad]

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

[gb]

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:

• Clustering
• quality filtering
• Smaller reference database
• USEARCH instead of blast(https://drive5.com/usearch/manual8.1/cmd_usearch_local.html)
• Using hmmer (http://hmmer.org/)

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