BRAT

BRAT aligns sodium bisulfite-converted short reads from the Illumina Genome Analyzer to determine DNA methylation patterns at single-base resolution.

Key Features:

• Support for Single and Paired-End Reads: Handles single-end and paired-end reads, including reads and mates of different lengths.
• Enhanced Speed and Accuracy: Provides improved speed and mapping accuracy, yielding higher numbers of uniquely mapped paired-end reads.
• Quality Control: End-trims low-quality bases from reads prior to mapping to improve reliability of mapped data.
• Nucleotide Count Reporting: Reports nucleotide counts for mapped reads against a reference genome to support methylation analysis.

Scientific Applications:

• Epigenetic profiling: Enables single-base-resolution DNA methylation profiling from bisulfite sequencing data.
• Gene regulation studies: Supports studies aimed at understanding gene regulation mechanisms via analysis of DNA methylation patterns.
• Disease association studies: Facilitates investigation of associations between DNA methylation patterns and disease.
• Developmental biology: Supports investigations of DNA methylation dynamics in developmental biology research.

Methodology:

Aligns bisulfite-converted short reads using algorithms that accommodate reads and mates of different lengths and integrates end-trimming of low-quality bases during the mapping process.