BS-Seeker2

BS-Seeker2 performs alignment of bisulfite-treated sequencing reads and generates base-resolution DNA methylomes for genome-wide DNA methylation analysis.

Key Features:

• Alignment of bisulfite-treated reads: Maps bisulfite-treated sequencing reads to reference genomes to enable base-resolution methylation calling.
• Enhanced mappability: Uses local alignment strategies to improve the mappability of bisulfite sequencing data compared with existing aligners.
• RRBS-specific indexing: Constructs specialized indexes optimized for Reduced Representation Bisulfite Sequencing (RRBS) libraries to improve mapping efficiency and accuracy.
• Conversion filtering: Filters reads with incomplete bisulfite conversion to reduce overestimation of DNA methylation levels.
• Comprehensive output formats: Produces BAM and WIG outputs and CGmap and ATCGmap file formats for full representation of DNA methylomes.
• Support for WGBS and RRBS: Handles both Whole Genome Bisulfite Sequencing (WGBS) and RRBS data for methylome generation.

Scientific Applications:

• Epigenetic research: Enables genome-wide DNA methylation analysis at base resolution for studies of epigenetic regulation.
• Gene regulation studies: Supports investigation of methylation-associated gene regulation and locus-specific methylation patterns.
• Clinical and disease research: Facilitates analysis of aberrant DNA methylation patterns in clinical and disease-related investigations.

Methodology:

Performs local alignment of bisulfite-treated reads, constructs specialized RRBS indexes, applies bisulfite-conversion filtering to remove incompletely converted reads, and outputs alignments and methylation profiles in BAM, WIG, CGmap, and ATCGmap formats.