bcbio-nextgen
Our NGS analyses rely on our bcbio.nextgen framework, a community-developed NGS workflow that comes with full documentation, is open source under the MIT license, and is in use at over a dozen sites internationally. It is installed at both the FAS and HMS Research Computing environments and provides researchers with best practice workflows for exome / whole-genome sequencing (built around GATK 3.0 and FreeBayes) , RNA-Seq (TopHat2/STAR, Sailfish/Salmon, edgeR/DESeq2/limma), and most recently, small RNA-seq, single-cell RNA-seq and the intial steps of ChIP-seq. Take a look at some of the key blog posts around bcbio:
More presentations about bcbio
Knowledgebase
Our team collaborates on an eclectic list of useful bioinformatic tips and tricks in our Knowledgebase
Conda
We also recommend conda as an easy way to install and run software in a shared environment without worrying about dependencies. Many general use packages can be found on Anaconda Cloud and bioinformatics software can be found through bioconda.
BioGrids
If you are working on the HMS RC cluster and need a piece of bioinformatics software, we recommend you look at the software available through BioGrids project, a software stack for bioinformatics available on HMS O2