Whole genome alignment and post-alignment analysis of sodium bisulfite treated DNA sequences are inherently inhibited by exceedingly large data sets, alignment algorithm complexity, and computational hardware limitations. Although there exist several pairwise and multiple sequence alignment programs, in addition to statistical analysis and quality assessment software tools, there currently is a deficiency in software that integrates these phases collectively, while concurrently increasing automation and enabling better curation of genomic data.

To solve these challenges, we created bspipe, a flexible Java 1.7 software pipeline for whole genome alignment of sodium bisulfite treated DNA with integrated quality control and statistical analyses. This software achieves the objectives of increasing automation, persisting data and metadata to a relational database, and integrating additional software tools.

Download the source code which is released under the Apache 2.0 license. Or, browse the core API. Check back for future updates, which will be posted here.