Bison

Bison aligns bisulfite-converted short-read sequencing data (e.g., whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS)) using distributed cluster computing to accelerate and support accurate DNA methylation analysis.

Key Features:

• Cluster Utilization: Distributes alignment workloads across multiple compute nodes to reduce processing time for large bisulfite sequencing datasets.
• Scalability (bison_herd): Provides a bison_herd variant that can operate across an arbitrary number of nodes to accommodate larger datasets and higher computational demands.
• Underlying Aligner: Uses bowtie2 as the underlying aligner for mapping bisulfite-converted reads.
• Library Support: Supports both directional and non-directional bisulfite sequencing libraries.
• Alignment Accuracy: Improves alignment accuracy to support reliable downstream methylation analysis.
• Helper Programs and R Integration: Includes helper programs and scripts for quality control and for preparing results for statistical analysis with R packages.
• Performance Acceleration: Reduces overall alignment time compared with single-node alignment approaches.

Scientific Applications:

• DNA Methylation Analysis: Enables rapid alignment of WGBS and RRBS data to support base-resolution methylation calling.
• Epigenetics Research: Facilitates large-scale epigenomic studies that require accurate mapping of bisulfite-converted reads.
• Cancer Biology: Supports methylation profiling in cancer studies where DNA methylation changes are informative.
• Developmental Biology: Assists studies of developmental gene regulation by enabling timely processing of bisulfite sequencing data.

Methodology:

Bison employs bowtie2 as its aligner, supports directional and non-directional bisulfite libraries, and distributes computation across cluster nodes via a message passing interface (MPI).