We use bcbio-nextgen for the analysis of sequencing data, mainly, (sc)RNAseq, smallRNAseq, DNASeq and ChIPSeq. It is not rare that we get collaborators who wants to re-analyze public data-set.
Inside bcbio, we have bcbio_prepare_samples.py
to help to merge multiple
files that belong to the same sample into one file to make easier the configuration
of bcbio. We extended this script to pull down data from GEO and
SRA repository.