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