BStools

BStools improves alignment and CpG-site coverage for bisulfite sequencing data by applying a sequential trimming-and-retrieving alignment approach to increase mapped reads and methylation call completeness.

Key Features:

• Sequential Trimming-and-Retrieving Alignment: Implements a sequential trimming-and-retrieving alignment strategy that iteratively trims reads and reattempts alignment to recover reads that initially fail to map.
• Improved Coverage of CpG Sites: Optimizes alignment to increase coverage of CpG sites for DNA methylation analysis, including data generated on platforms such as Illumina's NextSeq.
• Automated Analysis Toolkit: Provides an automated workflow for processing bisulfite sequencing reads, encompassing preprocessing and alignment steps to standardize analysis.

Scientific Applications:

• Epigenetic Research: Supports high-resolution DNA methylation profiling in epigenetic studies.
• Genome-wide Methylation Mapping: Enables comprehensive mapping of methylation patterns across CpG sites genome-wide.
• Gene Regulation Studies: Facilitates investigation of methylation-associated gene regulation.
• Development and Disease Mechanisms: Aids studies of development and disease mechanisms where DNA methylation is implicated.
• Illumina Bisulfite Sequencing Analysis: Applied to bisulfite sequencing datasets generated on Illumina platforms such as NextSeq.

Methodology:

Performs sequential trimming of bisulfite-treated reads to remove low-quality bases and adapters, attempts initial alignment, and subjects reads that fail to align to further trimming and iterative realignment (sequential trimming-and-retrieving alignment).