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anvi'o v2.3.2, "Ocean"
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@meren meren released this 20 Apr 01:42
· 14728 commits to master since this release
v2.3.2
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We are happy to announce the new version of anvi'o: "Ocean" (The code name for this release emphasizes our attachment for this fragile environment, and all of its inhabitants. This code name was suggested by @ShaiberAlon, and won the popular vote. Another suggestion was Samurai Champloo by @tdelmont, and although we all REALLY wanted it to win, it managed to get only a single vote. Real pity).

image

After 127 changes in the codebase that introduced more than 1,850 lines of code and removed 500, as usual, the current version includes many bug fixes, as well as some major changes. This release note will give you a summary of most important changes.

Splitting large anvi'o profiles into easy-to-share, self-contained, and fully functional pieces

We have always been interested in providing our users with the ability to share intermediate findings their analyses produce. However, if anvi'o profiles can get too large too quickly, and it was not possible to share only a subset of a profile.

Now it is possible to create individual, self-contained anvi'o profile and contig databases for bins stored in anvi'o collections (#482). This way, instead of sharing the entire profile database and contigs database, you can share only a single genome bin from your profiles. This is done by our new program anvi-split, which creates a very comprehensive subset of your metagenome. It is so comprehensive that everything that can be done with your full data (from visualizing your data interactively to displaying or investigating SNVs) can be done with this subset, as well.

Leaner auxiliary data files

Now anvi'o uses GZIP compression on HDF5 files, which results in approximately 5 times smaller auxiliary data files (b83f747). The best part? It is that it is backwards compatible!

A small gift for miners of single-nucleotide variants

The inspection page of the anvi'o interactive interface allows you to investigate mapping results in a comprehensive way. We have been looking at our inspection pages a lot, and it was always a pain to learn important details for a given single-nucleotide variant directly from the interface.

With this release (13f1fbd), you can click on those SNVs, and enjoy your new popup window that lists everything that is relevant:

yay

Single tear.

Storing anvi'o displays in batch mode like a pro

Have you ever had tens of bins that you would like to visualize in the anvi'o interactive interface and save what you see in a figure? We had to, and it required lots of manual work. So we implemented a new parameter (e467360): --export-svg. When you provide a file name to this parameter in your anvi-interactive call, and if you have a state called default in your profile database, you will get an SVG file! So this becomes totally possible to do:

anvi-refine -c CONTIGS.db -p PROFILE.db -C MY_COLLECTION -b MY_BIN --export-svg MY_BIN.svg

If you had read "Working with SVG files anvi'o generate" post, you also know that you can immediately convert this output into a PNG file, too:

inkscape --without-gui -f MY_BIN.svg --export-png MY_BIN.png -d 300 -D

Doing these two operations in a BASH loop allowed us to visualize all our bins in a recent project in a heart beat and create a figure like this with minimal effort:

image

If we can do this, think about what you can do!

While he was on this, @ozcan also fixed the alignment issue with our SVG outputs (f7cd4de) so our SVG exports center in Inkscape correctly.

More interface sweets

We know none of you use it, but we can now show samples and layer labels in phylogram view (#490) in case thats why you were not using it.

Also now you can use the shortcuts m and s to hide the settings and mouse panels (4447eec). The best part? They come back when you press them again! Magic.

Thanks to YOU

  • Thanks to Roxanne Beinart (@rbeinart), now anvi'o exports gene alignments in protein clusters (#494).
  • Thanks Damien Courtine (@dcourtine), anvi'o will no longer complain about the unavailability of IP addresses and stuff (#485).
  • Thanks to John Eppley (@jmeppley), anvi'o will not fail to close files it opens (#487).
  • When Joe Vineis (@jvineis) complained about the interface glitches when there are too many bins in a collection, @tdelmont suggested that we should tell him to not use anvi'o with too many bins. But we didn't listen to him, and fixed it (#491).
  • When Joe Vineis came back and told us that anvi-summarize tasks were failing when custom HMMs are used, @tdelmont suggested that we respond to him by asking him to not use custom HMMs with anvi'o. We didn't listen to him, and fixed it, too (#484). Now you know!

Installation or upgrade

Please do not use the binaries below, and visit our installation page for details:

http://merenlab.org/2016/06/26/installation-v2/

Questions?

Come join our discussion group!

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