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bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatics pipeline able to perform a full DNA methylation level analysis
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README.md

bicycle

bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatics pipeline able to perform a full DNA methylation level analysis. More info at the bicycle project page.

How it works?

bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatic pipeline aimed to analyze whole genome bisulfite sequencing data. It can process data from directional (Lister) and non-directional (Cokus) bisulfite sequencing protocols, and from single-end and paired-end sequencing, and performs methylation calls for cytosines in CG and non-CG contexts (CHG and CHH).

bicycle uses as input the bisulfite sequencing files from the different samples (FASTQ format) and a reference genome (FASTA format). It then performs: generation and indexing of Watson and Crick bisulfited versions of the reference genome, in-silico bisulfitation of sequenced reads, read alignment, error estimation in bisulfite conversion, identification of clonal and ambiguous reads, cytosine methylation detection in CG and non-CG contexts, with non-CG to CG context correction when appropriated, calculates methylation ratios, beta scores and weighted mean of cytosine methylation status, and performs genomic annotation of methylated regions, and differential methylation for cytosines (DMC) and genomic regions (DMR).

Requirements

Bicycle requirements:

  • Operating System: Linux/OSX
  • Java 1.8+
  • Bowtie1 aligner 0.12.7+ or Bowtie2 aligner 2.3.2+
  • samtools 0.1.8+

Coordinators

Authors

  • Daniel Glez-Peña (SING Research Group. Informatics Department. University of Vigo)
  • Osvaldo Graña (Bioinformatics Unit. CNIO: Spanish National Cancer Research Centre)
  • Hugo López-Fernández (SING Research Group. Informatics Department. University of Vigo)

License

  • GNU Lesser General Public License v3.0
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