Churros

Churros is a Docker-based epigenomics analysis pipeline. While Chross mainly focuses on the ChIP-seq analysis, it can also handle CUT&TAG, ATAC-seq and DNA methylation data.

Tools installed in Churros

The latest version of Churros uses the following tools internally.

  • Mapping
    • Bowtie v1.3.1

    • Bowtie2 v2.4.5

    • BWA v0.7.17

    • chromap v0.2.4

  • ChIP-seq analysis
    • MACS2 v2.2.9.1

    • DROMPA+ v1.18.0

    • SSP v1.3.0

    • ROSE v0.1

    • ChromHMM v1.24

    • ChromImpute v1.0.3

    • epilogos v0.1.2

  • ATAC-seq analysis
    • TOBIAS

    • HINT-ATAC

  • Bisulfite sequencing (DNA methylation)
  • Differential analysis
  • Functional analysis
  • Quality assessment
    • FastQC v0.11.9

    • fastp v0.23.2

    • MultiQC v1.12

  • File processing
  • Adapter trimming
  • Mappability calculation
  • Utility tools

Contents:

Contact:

Mail:

rnakato AT iqb.u-tokyo.ac.jp