At the interface of science and computing

Repo of the Week - Feb 9, 2013

So the Repo of the Week didn’t quite pan out weekly, but I am going to keep the category going.

This weeks repo (well, pair of repos) comes to you courtesy of the Dunn lab. The two repos are biolite and agalma. What are these?

BioLite is a bioinformatics framework written in Python/C++ that automates the collection and reporting of diagnostics, tracks provenance, and provides lightweight tools for building out customized analysis pipelines. It is distributed with Agalma, but can be used independently of Agalma.

Agalma is a de novo transcriptome assembly and annotation pipeline for Illumina data. Agalma is built on top of the BioLite framework. If you have downloaded Agalma+BioLite, the files that are specific to the Agalma pipeline are located in the agalma/ subdirectory.

The authors have also made an Amazon EC2 image available with Agalma and all its dependencies. There is a tutorial to get things working on EC2.