@meren meren released this Jul 29, 2016 · 4330 commits to master since this release

Assets 2

Among various bug fixes over the latest stable release, v2.0.2 has multiple important improvements thanks to Özcan's efforts. I would also like to thank Julie Meyer, Patricio Geraldo, C. Titus Brown, Mohamed Amine Chebbi, Cody Sheik, and David Needham for their help, suggestions, and reports that improved the code base.

Here are some of the notable changes for v2.0.2:

Up to 400% performance increase for the interactive interface

Now numerical layers in the anvi'o interactive interface use a single path, which decreases the number of SVG objects dramatically without any remarkable visual distortion (#381). With this improvement, the number of objects in the Infant Gut Dataset go from 59,090 to 17,984, and looks as good as ever. This change will not improve numerical layers visualized in intensity mode.

More distance metrics and linkage algorithms for hierarchical clustering operations

Anvi'o has always used euclidean distance with ward linkage for hierarchical clustering. Now these defaults can be changed in any relevant program using generic parameters --distance and --linkage (#377). Here is a list of available distance metrics,

['euclidean', 'cityblock', 'sqeuclidean', 'cosine', 'correlation', 'hamming',
'hamming', 'jaccard', 'chebyshev', 'canberra', 'braycurtis', 'yule', 'matching',
'dice', 'kulsinski', 'rogerstanimoto', 'russellrao', 'braycurtis', 'yule',
'matching', 'dice', 'kulsinski', 'rogerstanimoto', 'russellrao', 'sokalmichener',
'sokalsneath', 'minkowski']

and linkage methods,

['single', 'complete', 'average', 'weighted', 'centroid', 'median', 'ward']

Import / export functionality for anvi'o interactive interface states

Anvi'o interactive interface states are files that hold visual settings of a project, and are stored in the profile databases. Now these states can be exported, and imported with two new programs, anvi-export-state and anvi-import-state. This way visual attributes can be edited manually or programmatically (#382).

Better documentation for importing external gene calls

So you will less likely get lost while trying to import your own gene calls while generating an anvi'o contigs database if you don't want to go with Prodigal.

anvi-summarize works again!

Cody and Needham found out (link) that there was a bug affecting anvi-summarize when external binning results are imported into an anvi'o profile database. The bug is no more (#380).

Setting taxonomic levels to display

All interfaces focused on species-level taxonomy when taxonomical annotations were available in an anvi'o contigs database. We have now added a new generic parameter, --taxonomic-level, so you can specify which taxonomic level you would like to focus on in appropriate interfaces (i.e., while displaying a project or when summarizing a collection).

Anvi'o appeared in the second ECOGEO Workshop on Environmental 'Omics as a platform to benchmark various approaches for metagenomic binning.

image

The anvi'o tutorial I used for this workshop will soon be available online.

Thank you for your interest!


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