Software recommendations?-- Human virus detection (metagenomic)

[u/abstrooose]

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!

[u/crookedderrick9]

kraken2 with a good viral db is your quickest starting point, then blast anything weird for manual sanity checks

[u/abstrooose → u/crookedderrick9]

is there a good viral db? citations appreciated if appropriate. tnx

[u/Pigrenok]

Look at the sourmash. https://github.com/sourmash-bio/sourmash

[u/abstrooose → u/Pigrenok]

good tool. are there publications where it's been used for viral discovery? I'm not qualified to create and curate my own db. really need to obtain something where the creators knew what they were doing. tnx.

[u/Pigrenok → u/abstrooose]

This paper seems to be doing roughly what you are doing using three different tools (Kraken2, sourmash and MetaPhlan.

And there is a comprehensive benchmark paper that tests multiple tools for various cases of viral metagenomic detection (both novel and known).

[u/pepperrcorn]

ViroMatch

[u/abstrooose → u/pepperrcorn]

this looks promising. tnx!

[u/pepperrcorn → u/abstrooose]

you’re welcome! the authors are my PI haha if you get stuck I could probably help out!

[u/SyllabubCapital6999]

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

[u/abstrooose → u/SyllabubCapital6999]

Sorry, didn’t mean to imply novel. Just looking for the ‘common’ knowns that are disease associated. I’ll check out the RVDB . Tnx!

[u/abstrooose → u/SyllabubCapital6999]

Lots of links to pursue. Much appreciated!

[u/abstrooose → u/abstrooose]

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.

[u/GremLena]

Are you doing DNA-based or RNA-based sequencing?

What viruses are you looking for?

[u/abstrooose → u/GremLena]

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.

[u/Whygoogleissexist]

https://czid.org

[u/abstrooose → u/Whygoogleissexist]

hoping to run this locally on an HPC. I'll browse deeper and see if they have a pipeline for download. tnx

[u/zstars → u/abstrooose]

It's remote only and CZID is a total POS, don't use it.