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BS-Seeker3: ultrafast pipeline for bisulfite sequencing
Kevin Yu Yuan Huang1,2, Yan-Jiun Huang1, Pao-Yang Chen3
1Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
BMC Bioinformatics
|April 5, 2018
Summary
BS-Seeker3 is an ultra-fast bioinformatics pipeline for analyzing DNA methylation data from whole-genome bisulfite sequencing (WGBS). It offers high accuracy and mappability, significantly improving epigenome sequencing analysis speed.
Area of Science:
- Epigenetics
- Genomics
- Bioinformatics
Background:
- DNA methylation is a key epigenetic modification regulating gene expression and inheritance.
- Whole-genome bisulfite sequencing (WGBS) estimates DNA methylation at single-nucleotide resolution.
- Existing WGBS analysis tools are often too slow for current research demands.
Purpose of the Study:
- To develop an optimized and efficient pipeline for processing bisulfite sequencing data.
- To address the need for faster analysis in epigenome sequencing.
Main Methods:
- BS-Seeker3 is an improved implementation of BS-Seeker2.
- It leverages standard bioinformatics lab computational power for ultrafast alignments.
- Incorporates all alignment features of BS-Seeker2.
Main Results:
- BS-Seeker3 achieves ultrafast alignment speeds.
- Demonstrates high accuracy and mappability, exceeding other evaluated aligners.
- Provides seamless integration with the MethGo analyzer for diverse epigenomic analyses.
Conclusions:
- BS-Seeker3 is an accurate, versatile, and ultra-fast pipeline for bisulfite-converted reads.
- Facilitates efficient DNA methylation data analysis and visualization.
- Supports up to 9 types of genomic and epigenomic analyses.
