anvi'o v3, "Eden"
We are happy to announce a new version of anvi'o, "Eden".
After more than 300 changes that introduced about 6,000 new lines, and removed about 2,250 from the anvi'o codebase, the current version includes many bug fixes, as well as some new features. This release note intends to give you a summary of most important changes.
The codename, which was suggested by @watsonar and won the popular vote, is to mark the arrival of the newest honorary member of our lab. Despite her very young age which doesn't even round to a positive integer, she managed to tip the scale of the gender diversity in our lab for the better. We thank Alon and Rebecca for allowing us to witness essential beauties of life through their happiness.
A new program: anvi-display-contigs-stats
Thanks to @ozcan's recent efforts, anvi'o now can give you basic stats about your contigs databases. Using anvi-display-contigs-stats you can generate insights from one or more contigs databases. Beyond obvious uses, we hope it to be useful to interactively compare different assemblers on the same dataset, or multiple genomes for each of which you have a contigs database.
Since a basic framework is now in place for such comparisons, we will be looking forward to hearing suggestions from anvi'o users to improve it further at every chance.
Here is what you see when you run it on the contigs database of our FMT study:
anvi-display-contigs-stats FMT-CONTIGS.db
And this is what you see when you run it on a bunch of single genomes:
anvi-display-contigs-stats c0328-Microgenomates.db \
c0319-Microgenomates.db \
c0091-Candidate_CPR3.db \
c0205-Parcubacteria.db \
c0661-Parcubacteria.db \
c0792-Candidate_WS6.db
We hope you try it on your current contigs databases, and let us know about your suggestions.
A new versioning approach
We will no longer follow the standards of semantic versioning with anvi'o releases. The last anvi'o version was v2.4.0, this one v3, and the next one will likely be v4, unless there is an absolutely minor change that will not require you to update your v3 installation.
Why leaving the field standards? Anvi'o is an essential tool for us to do science, and we know of multiple other groups besides our's that also use this platform quite rigorously to go after their own questions. Since this is not a media player, which would continue to play your favorite shows even if you don't keep it up-to-date, and since the excellence of everything we do with anvi'o depends on its accuracy, we want our users to update their installations every time there is a new version. When this is the case, the conventional versioning of software becomes rather irrelevant, and somewhat confusing. We are aware of the fact that installing and updating software could be quite a frustrating task, and we do our best to improve those steps for you. If you have any questions or suggestions, please send them to the anvi'o discussion group.
Making a release is quite a painful process, and I personally hate it passionately as it takes at least a full day from my life. We are only doing it when there is a need for it. So, please keep your anvi'o up-to-date while @ozcan, myself, and other developers and contributors do their best to try to keep it bug free for you :)
Bug fixes, new anvi'o programs, and new flags
This version includes a large amount of bug fixes and minor improvement of available programs with additional flags.
New programs that became available with this release include anvi-delete-state, anvi-display-contigs-stats, and anvi-export-samples-db.
We also added new scripts to anvi'o distribution, such as anvi-script-add-default-collection (to add a quick 'default' collection to access to all splits in a profile database, and anvi-script-filter-fasta-by-blast (to remove weak hits from BLAST search outputs).
Some of the new flags we added to our existing programs include --return-codon-frequencies-instead to be able to get codon frequencies instead of amino acid frequencies from BAM files via anvi-get-aa-frequencies, --items-order to explicitly provide an items order to anvi-interactive, --max-num-genes-missing-from-bin and —min-num-bins-gene-occurs to remarkably improve the functionality of anvi-get-seqeunces-for-hmm-hits to filter weak genomes or genes for better phylogenomic analyses thanks to Ryan Bartelme's suggestions, and --align-with flag so we can optionally use FAMSA instead of muscle, which works exceptionally better than muscle in our experience to align sequences within our protein clusters. We heard FAMSA thanks to Antonio Fernandez-Guerra.
Contigs database version bump
We realized that were. You will be able to update your existing contigs databases without any pain via the upgrade script anvi-script-upgrade-contigs-db-v8-to-v9.
Genome storage version bump
We extended the functionality of anvi'o genome storages that are used for pangenomic workflows. They now also keep a copy of every gene they describe in DNA alphabet. Unfortunately this also requires an update, which can be done via anvi-script-upgrade-genomes-storage-v3-to-v4.
Thank you for your interest in anvi'o!
Please find anvi'o tutorials and installation instructions here: