DNAdye

DNAdye is an open-source software package for analyzing DNA sequencing data, with a focus on DNA methylation profiling. The project provides end-to-end support for preprocessing, methylation extraction from bisulfite sequencing data, differential methylation analysis, and visualization, integrating with common bioinformatics workflows.

Implementation and license: DNAdye is implemented primarily in Python, with performance-critical components written in C++. It runs on Linux and macOS, with community-provided builds for Windows. The project is released under a permissive open-source license to facilitate redistribution and collaboration.

Key features include quality control and trimming, alignment evaluation, methylation calling, statistical testing for differential methylation, and interactive or static visualization of methylation patterns. It supports standard file formats such as FASTQ, BAM, and BED, and can export results to widely used formats for downstream analysis.

Development and reception: DNAdye originated as a collaborative effort among research groups to streamline methylation analysis workflows. Since its initial release, it has seen multiple community contributions, plug-ins, and tutorials. The project emphasizes reproducibility, with documentation, example datasets, and test suites.

DNAdye is often used alongside established tools such as Bismark and BS-Seeker for comprehensive methylation analysis.