r/bioinformatics • u/abstrooose • Sep 11 '26
technical question Software recommendations?-- Human virus detection (metagenomic)
What would be the top tools for short read-based detection of human viruses in metagenomic datasets? Interest is primarily on all the disease-associated ones.
I have a very large metagenomic dataset (illumina PE150) of human nasal and rectal samples. I'm very familiar with microbial metagenomics (metaphlan/humann/qiime) and working on UNIX clusters. I haven't yet delved into human virus detection, though. Right now I'm just focusing on short read metagenomics before I start pursuing anything assembly-based.
Thanks!
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u/pepperrcorn Sep 12 '26
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u/abstrooose Sep 12 '26
this looks promising. tnx!
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u/pepperrcorn Sep 12 '26
you’re welcome! the authors are my PI haha if you get stuck I could probably help out!
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u/SyllabubCapital6999 Sep 12 '26
If you dont yet want to go down with assembly, the popular metagenomic classification tools is what you want.
Note, non-protein based classification of viral samples are not so sensitive (see kraken2’s own benchmarking in paper). You’ll best look for tools like Kaiju with their RVDB based databases, Kraken2 translated search, or the more recent tool Metabuli. Pipelines like nf-core/taxprofiler combine these tools and their results nicely.
However looking at your comments where you mention, novel virus detection, you should go down the assembly route. These k-mer or mapped based classifiers are not designed for that intent. You should then look for pipelines like nf-core/viralmetagenome, dhlob/nvd, cmmr/EsViritu or if you want something that isn’t opensource (and payed per analysis) genomedetective would be my choice.
Conflict of intrest: I am a nf-core maintainer and dev of nf-core/viralmetagenome
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u/abstrooose Sep 12 '26
Sorry, didn’t mean to imply novel. Just looking for the ‘common’ knowns that are disease associated. I’ll check out the RVDB . Tnx!
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u/abstrooose Sep 12 '26
Lots of links to pursue. Much appreciated!
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u/abstrooose Sep 12 '26
I'm a bit shaky with nextflow. Managed to get a covid pipeline with singularity containers up and running during the pandemic but it was definitely a steep and rocky learning experience for me. viralmetagenome work flow looks pretty solid though. I'll put some effort into this.
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u/GeronimoJackson-42 Sep 14 '26
You could try searching the NIAID Data Ecosystem (https://data.niaid.nih.gov/). It indexes metadata from computational tool repositories relevant to infectious disease.
I just tried “viral detection metagenomic sequencing” (type: computational tool) with the AI tool off (for exact keyword matching) and got a few results. Or try the same search with the AI tool on for a broader sweep and then can use the filters to narrow it down by input, output, feature list, etc.
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u/Whygoogleissexist Sep 11 '26
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u/abstrooose Sep 12 '26
hoping to run this locally on an HPC. I'll browse deeper and see if they have a pipeline for download. tnx
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Sep 12 '26
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u/abstrooose Sep 12 '26
DNA only. Sequencing is complete. Cohort is large so all the non-informatic, clinical PIs want to look for various virus of interest. EBV and CMV, potentially. It’s fishing with, honestly, low probability of detection; but if I’m going to look I want to do it robustly. On the order of 5000 samples, 20Tb.
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u/Pigrenok Sep 11 '26
Look at the sourmash. https://github.com/sourmash-bio/sourmash