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bisulfiteSeqTools.md

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Bisulfite Sequencing Analysis Tools

Quality Control

  • BSeQC --- SAM/BAM files | Publication
  • trim_galore --- for RRBS experiments
  • FastQC --- additional quality control
  • MethyQA --- FastQC + BRAT[tool] alignment, methylation ratios at cytosine sites | Publication

Mapper

  • Bismark --- seems to be the tool to use | Publication | URL
  • Bison --- similar to bismark, runs on a cluster, needs MPI | URL
  • BS Seeker --- Publication | URL
  • BSmap --- URL (Jan 2013)
  • segemehl --- with gaps | Publication | URL
  • Bicycle --- from mapping to methylcytosine | URL

After Mapping

  • GBSA --- input from BSmap, BS Seeker, RRBSmap | Publication | URL
  • methylKit --- URL

Pipeline

  • MethPipe --- pretty new | URL
  • BiQ Analyzer HT --- Java Web Start | Publication | URL

Other

  • MethylCoder ---
  • BISMA ---
  • BSmooth --- Don't think it's up-to-date | URL

MISC