• MethCP

• Referenced in 1 article [sw28729]
• Detection with Change Point Models. Whole-genome bisulfite sequencing (WGBS) provides a precise measure...

• GATK

• Referenced in 17 articles [sw12019]
• The genome analysis toolkit: a MapReduce framework for...

• Samtools

• Referenced in 22 articles [sw14583]
• Samtools is a suite of programs for interacting...

• FastQC

• Referenced in 8 articles [sw16946]
• FastQC: A quality control tool for high throughput...

• FASTX

• Referenced in 2 articles [sw17090]
• The FASTX-Toolkit is a collection of command...

• Trimmomatic

• Referenced in 6 articles [sw17091]
• Trimmomatic: a flexible trimmer for Illumina sequence data...

• Cutadapt

• Referenced in 2 articles [sw17303]
• Cutadapt removes adapter sequences from high-throughput sequencing...

• BS Seeker

• Referenced in 6 articles [sw23481]
• BS Seeker: precise mapping for bisulfite sequencing. BACKGROUND...

• BSmooth

• Referenced in 11 articles [sw23483]
• BSmooth: from whole genome bisulfite sequencing reads to...

• Bismark

• Referenced in 5 articles [sw23504]
• Bismark: a flexible aligner and methylation caller for...

• BSMAP

• Referenced in 5 articles [sw23515]
• BSMAP: whole genome bisulfite sequence MAPping program. BACKGROUND...

• VarScan

• Referenced in 8 articles [sw27471]
• VarScan is a tool that detects variants (SNPs...

• Bowtie 2

• Referenced in 20 articles [sw29190]
• Bowtie 2 is an ultrafast and memory-efficient...

• mrsFAST

• Referenced in 2 articles [sw29574]
• mrsFAST: a cache-oblivious algorithm for short-read...

• MethylCoder

• Referenced in 2 articles [sw35177]
• MethylCoder: software pipeline for bisulfite-treated sequences. Motivation...