• 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...