Anvi'o v2.0.0
6 months and 955 commits later anvi'o v2 is ready for prime time!
We fixed many bugs, and we further solidified the foundation of the platform. It would be nearly impossible to list all changes, hence in this late release note I will only mention things that I found important.
A new pangenomic workflow
Which requires you to install almost nothing, and allows you to combine metagenomic bins you identified from your samples with genomes from elsewhere seamlessly with the new program anvi-pan-genome. Please see the updated tutorial:
http://merenlab.org/2015/11/14/pangenomics/
An anvi'o server for data visualization
Now you can use anvi'o to visualize any tabular data, organize its layers, add normalizations, set colors, save your work, and share it with others publicly or privately through http://anvi-server.org.
Please see the documentation of the anvi'o interactive interface and data types it works with:
http://merenlab.org/2016/02/27/the-anvio-interactive-interface/
Here is a tiny demo for you:
http://anvi-server.org/public/meren/interface_demo_VII
And here is a hint for geeks: anvi-push -h
We thank Tobi Paczian for anvi-server, who temporarily joined us, and worked relentlessly and exclusively on the server interface.
A new mode for anvi'o interactive interface: "collection"
Until now there were three modes to run the interactive interface: full mode, refine mode, and manual mode. With the new collection mode, you can use the anvi'o interactive interface to show metagenomic bins in a given collection and their distribution across your samples instead of individual contigs.
More here: #359
A more comprehensive infrastructure to characterize single-nucleotide variants
Anvi'o does a much better job at profiling and reporting SNVs, and generating very comprehensive outputs through which you can query SNVs with extensive control. A tutorial is here: http://merenlab.org/2015/07/20/analyzing-variability/
Related issues addressed: #274, #364, #367, #324, #309
Better utilization of external gene calls
Anvi'o now uses Prodigal by default to identify open reading frames in contigs upon the generation of the contigs database. Which allows us to do much more with open reading frames and gene calls. But we also improved making room for the user to import their own gene calls. See anvi-gen-contigs-database -h.
Better documentation
Please see the updated anvi'o project page with new and updated tutorials:
http://merenlab.org/software/anvio/
A new sticker for anvi'o
Yes! It is true:
Come say hi to us in Montreal during the ISME conference, and we will secretly put one in your pocket.
Please don't install the new version using the archive files below. Instead, try one of these:
Installing from source | Installing via PyPi | OS X installer | Docker image