anvi'o v2.4.0, "Pyrenees"
We are happy to announce the new version of anvi'o, "Pyrenees".
After 350 changes in the codebase that introduced more than 4,500 lines of code and removed about 9,000, the current version includes many bug fixes, as well as some important additions to the repository. This release note will give you a summary of most important changes.
The codename is to honor our friend and colleague, Tom Delmont, who is going to continue working with us from France. The Pyrenees is a mountain range in southwest Europe between France and Spain, where Tom spent most of his life.
Single-amino acid variants (SAAVs)
Since its very first version, anvi'o has been providing you with one of the most comprehensive frameworks to make sense of single-nucleotide variants (SNVs). Here is a tutorial for skeptics.
Although it has been in anvi'o for more than a year, we are very excited to officially announce the anvi'o workflow to investigate single-amino acid variants. More resources on SAAVs will soon be available, and we will keep you posted. But if you have been using the anvi-gen-variability-profile program to characterize single-nucleotide populations in your population genomes, all you need to do now is to add --engine AA to get single amino acid profiles.
Fluency in phylogenomics
Anvi'o now can speak phylogenomics. Here you will find an extensive tutorial with reproducible examples:
http://merenlab.org/2017/06/07/phylogenomics/
You now can do phylogenomic analyses in anvi'o for metagenomic bins or pangenomes thanks to others who pushed us for it. Luke McKay of the Montana State University asked for gene concatenation for HMM hits in genomes from metagenomes, we delivered it, (47fd334, b9780a5, 29a3827, 3ee670e, fa7128a). Then, Ryan Bartelme of the University of Wisconsin-Milwaukee asked for concatenated genes in protein clusters of pangenomes by sending a private e-mail, and we delivered it, too (1726476, 3d07e8b, 99359bc). We didn't stop there. We implemented a simple driver for FastTree (227e892) for starters so you can immediately start playing with your data. As always, we are thankful for your suggestions.
Identifying ribosomal RNAs everywhere
In most cases, getting ribosomal RNA genes out of isolate or metagenome-assembled genomes is not as straightforward as one would like, even when the assembler managed to assemble them.
Gene callers usually don’t perform well when it comes to identifying 16S or 23S rRNA genes, and using primer sequences for these regions is not exactly 2017. We added a new feature in anvi’o that reduces the recovery of rRNA gene sequences from isolate, single-cell, or metagenome-assembled genomes to a couple of key strokes. More information and examples are here:
http://merenlab.org/2017/07/09/recovering-rRNAs/
The small but mighty 'push' button
This is something we are very excited about. You know how sometimes you have something on your interactive interface you would like to show to your colleagues, or share with everyone on the planet? Well, with this version you will be able to click on this little new cloud button on the interface,
and you will be able to send your interactive display directly to http://anvi-server.org or any other anvi'server instance online. After which you can share this interactive display in read-only mode privately with your colleagues, editors, or reviewers, or with everyone by making it public.
Here is an appropriate use of it in a recent paper in Cell Reports that gives another dimension to a static figure:
https://www.youtube.com/watch?v=WtPB9GchuEI
More functional side buttons
Now we have a way to deliver some important news to your door step:
More information on this new addition, including notes about possible privacy concerns is here:
http://merenlab.org/2017/05/16/anvio-news-panel/
Please consider sharing your thoughts and opinions on this.
We also made sure anvi'o can convey extensive descriptions of the displays shown in anvi'o. Here is an example:
The description tab gives access to an editor, in which you can describe the data using Markdown syntax. We hope that this practice catches on, so whenever someone looks at an anvi'o display, they know that there will be some information on the side panel to better understand the details.
Please find anvi'o tutorials and installation instructions here: