1.0.2

Apart from minor bug fixes:

• anvi-populate-collections-table program is no longer in the codebase. Instead, we now have a better version of anvi-import-collection to import external binning results into our databases (#189).
• anvi-experimental-organization is also revamped (#148). This is the program we use to try different clustering configurations (for instance, you merge metagenomes and metatranscriptomes, and want to order contigs only based on their distribution across metagenomic samples --see this blog post for a good example). It stored clustering of contigs for a given recipe into a newick file, but now it can update the database if requested.
• @caglar10ur has pushed us lazy anvi'o developers to generate docker images for the platform by committing an initial Dockerfile into the repository (#191). More information on the docker image can be found via #193.

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(Please don't install the new version using the archive files below. Instead, take a look at the installation instructions

Minor bug fixes, and a new program: anvi-get-short-reads-from-bam

Besides a bunch of minor fixes (i.e., 90e4400, 8da7de0, 87347f6), we have two major changes:

• Anvi'o now has a new program, anvi-get-short-reads-from-bam, that reports all short reads from a BAM file, or from multiple BAM files, for a given bin. More information is available under issue id #173.
• There is no more version dependency for SciPy, which makes pip installation more straightforward.

(Please don't install the new version using the following archives. Instead, either use pip to install the new version, or download the latest source distribution from https://pypi.python.org/pypi/anvio).

Anvi'o 1.0.0

The very first release of anvi'o 1.0.0.

In this version there are some major additions to the release candidates:

• Anvi'o now has a completely redesigned interactive interface (#176). You can take a look at it here: http://umkk2268fc06.merenbey.koding.io:8080 (this link may not be working if you are from the future, but even then you may be able to find a link to a running demo here).
• We are no longer using the term "contamination" to describe to multiple occurrence of single-copy genes. If there are multiple hits to a single-copy gene, it is considered "redundancy" now (which was Jed Fuhrman's suggestion mostly to avoid confusion and panic, since "contamination" is a very troublesome word for microbiologists) (#177).
• Now anvi'o stores sequences for HMM hits against both for single-copy and non-single-copy gene HMM profiles in the summary (#174).
• Anvi'o now uses a more recent version of pysam (#179).

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With this release we started using git submodules for external projects that we rely on (such as d3.js, or bootstrap). Which makes these zip files almost useless, since GitHub does not include the source code for submodules in release archives.

This means, if you download the zip file for this release and install anvi'o, it will not be a fully functional installation.

In the future I will resolve this problem by uploading release archives to pip, and share links to those archives in these releases. If you want to install this beta, do this in your terminal after removing your old anvi'o codebase:

git clone --recursive https://github.com/meren/anvio.git
cd anvio
sudo python setup.py install

The second release candidate

Maojor changes from v1.0.0-rc.1

• We have a new program called anvi-get-sequences-for-hmm-hits that gives access to the raw sequences of HMM hits in a given bin, or collection of bins (#174).

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Please see instructions in https://github.com/meren/anvio/releases/tag/v1.0.0-rc.1 to upgrade your databases if you are switching to this version from 0.9.2.

The very first release candidate

Maojor changes from v0.9.2

• We now have an --additional-view parameter for anvi-interactive for experimentalists (#160).
• anvi-refine's interface capabilities are no longer limited (#165).
• JSON objects for interactive interface states are now stored in the profile databases (#170).
• The charts page now inherits samples' colors and their order from the main interactive interface (24dc9a2).
• There are improvements in the annotation database structure to facilitate easier access to HMM hits between (1ff27c6).

How to upgrade your anvi'o DBs

Structural changes in the annotation and profile databases resulted in bumps in their version numbers, which means your previous annotation and profile databases will not be compatible with this new version of anvi'o.

However, we implemented two programs that will upgrade your databases from latest current versions. This way you will not have to re-profile your samples. These two programs can be found in the sandbox directory:

• sandbox/anvi-script-upgrade-annotation-db-v2-to-v3
• sandbox/anvi-script-upgrade-profile-db-v4-to-v5

Here is how to run them:

$ /path/to/anvio/source/sandbox/anvi-script-upgrade-annotation-db-v2-to-v3 ANNOTATION.db
* The annotation database successfully upgraded from version 2 to 3!
$ /path/to/anvio/source/sandbox/anvi-script-upgrade-profile-db-v4-to-v5 PROFILE.db
* An empty states table is generated.
* 1 state files added to the database.
* Database successfully upgraded.

Please do not forget to backup your databases before running these.

A new display: Intensity

Thanks to @ozcanesen's efforts, we now have an additional display to our standard bars: intensity. New buttons in the interface facilitates the switch between the two displays. We can also use a grid for bin selection panels, instead of colors. A couple of example figures follow (using Sharon et al.'s infant gut dataset for historical reasons).

Here is the standard bar display with bins as a reminder:

This is the new intensity display:

And this is when the grids are turned on:

New program: anvi-import-collection

Along with a bunch of bug fixes,

• wow we have a new program anvi-import-collection (#157),
• we can summarize single profiles properly (#155),
• even when profile directories are moved around we can merge them without running into relative path issues (#154),
• and the MOST IMPORTANT OF ALL, the default message color in standard info outputs is now cyan, instead of blue (4d1b47a) ... while the rest of the human race will weep quietly, some of us who still use crappy terminals will be utterly happy.

SUMMARY += HMMs! Yay!

Apart from some minor bugs that are fixed,

• @ozcanesen changed the state version number, so say goodbye to your old state files. Yes, you heard that right. But with this new design, state files are going to be extremely re-usable regardless of adding or removing layers in the interactive interface through parameters such as --additional-metadata or --split-hmm-layers.
• We now have DNA sequences for open reading frames reported in the functions matrix in the summary. Summary is just lovely. I keep summarizing stuff.

We are getting there!

Summary += Functions!

With this new release, summary reports functions along with gene coverages.

Should be rigorously tested to make sure what it reports and the way it reports it makes sense.

An internal release

A couple bugs are fixed. Plus we have a new flag that will be COMPLETELY useless for the end user, but it is important for debugging and quick merging of very large datastets: --skip-merging-summaries (for anvi-merge).