The BWASP repository encompasses code and scripts developed in the Brendel Group for analyses of bisulfite sequencing data. The entire workflow relies on various other open source software as well as R scripts from the companion BWASPR repository. The code conforms to our RAMOSE philosophy: it generates reproducible, accurate, and meaningful results; it is open (source) and designed to be scalable and easy to use.

Input to the BWASP workflow consists of accession numbers or fastq files of bisulfite-sequencing reads as well as the appropriate genome assembly (and, if available, genome annotation). Output (after read quality control and mapping) are *.mcalls files that list the sufficiently covered genomic Cs and their methylation percentage in the given sample. The scripts in the bin directory take care of minor tasks in the overall workflow, but configuration and execution is via GNU make using edited copies of the makefiles provided in the makefiles directory. All the BWASP dependencies are encapsulated in a Singularity container available from Singularity Hub. Thus, once you know what you are doing, execution could be as simple as

singularity pull --name bwasp.simg shub:https://BrendelGroup/BWASP
singularity exec bwasp.simg make

(assuming you have prepared a suitable makefile in your working directory).

Please find detailed installation instructions and options in the INSTALL document. Once all preparatory steps are taken care of, see the HOWTO document for a complete example of how to implement and run a workflow.

Amy L. Toth, Murat Ozturk, Saranya Sankaranarayanan, and Volker P. Brendel (2018) Estimating the size and dynamics of the CpG methylome of social insects. To be submitted.

Please direct all comments and suggestions to Volker Brendel at Indiana University.