Looking for recommendations for a tool or #pipeline for binning of metaviromic reads. Anyone?
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Marco van Zwetselaar
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Bioinformatician and FOSS developer
@emiller yes! 🙂 Great to hear - and fun to read back my own peeves from 2 years ago 😄
@dsmith @naturepoker A big plus of giving a hands-on "how we dunnit" walkthrough is that it doesn't take a lot of preparation.
Recently had several lightbulb moments while Matt Cotten _a l'impromptu_ walked through how he came up with the "Entebbe primers".
It's tough to cater to an audience with huge variance in experience, but with a hands-on demo there's usually something to take away for everyone.
@fabiomarroni the binning isn't crucial - and technically the byproduct of mapping anyway 🙂 - just hoped to be able to assemble some bins. But the issue with #metavirome (targeting RT RNA) is always the competition with all that host & bacterial DNA.
@naturepoker I warmly recommend taking the UCSD course by Pevzer and Compeau that others mentioned here.
Rosalind, Stepik, and the Bioinformatics Algorithms books are all interlinked with it.
@dsmith thanks, taking a look at Cenote-Taker2.
Also found https://github.com/putonti/virMine but somewhat baffled by how it is set up: to run it you build a Docker image with the input files baked into it 🧐 .
That's taking #reproducibility to a whole new level.