dnmtools project

I am a committer to dnmtools, a software suite, written primarily in C/C++, for the analysis of DNA methylation data. My role in this project was to improve the efficiency of some of the tools, and I enjoyed the learning! Here is the list of my commits.

Formatting alignment files

Computational biologists often work with large files of DNA sequences, and it is important that these files are formatted correctly. In the context of DNA methylation data, we work with alginment data we call reads. These reads are aligned, or mapped, to the reference genome, and the alignment data are stored in SAM/BAM format. This is accomplished by dnmtools abismal. We further process the alignment data using dnmtools format to format the the mapped reads for downstream analysis. My first task was to improve the efficienty of dnmtools format. I wrote the details in my blog. The outcome was about 30 % reduction in computation time, which can be a lot when you are working with large files.