Anvi’o

anvi’o, the binning and visualization pipeline, is supposed to be THE COOLEST.  Here’s their methods paper.

We found that it is ridiculously easy to install on a mac, which is a big help, but it requires approx 40 GB per sample, so it probably won’t run in a timely manner on a laptop. Profiling is the most memory and time intensive part.

To use anvi’o you need to have contigs and mapping before you try to bin into genomes. The tutorials (and other documentation) provided on their website are pretty good, even walking you through the pre-anvio steps.

One really helpful feature is that it plays nice with other software, allowing you to include taxonomic and functional annotations from the method of your choice to your visualization. Anvi’o includes CONCOCT in its pipeline, but you can import bins you made with other software to compare and visualize.

And, bonus, they now have scripts to perform cpr searching!!

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