Dependencies#

This workflow relies on the following tools being installed and accessible by your system PATH. We recommend that you install FinaleToolkit through pip and the other packages through conda in the Bioconda channel:

  • finaletoolkit: A command-line tool for epigenomic feature extraction.

  • snakemake: A workflow engine that determines which operations (“rules”) to carry out on genomic files.

  • bedtools: A suite of utilities for working with and manipulating genomic intervals.

  • htslib: A library that includes bgzip, necessary to GZIP uncompressed BED files.

  • samtools: A set of tools for manipulating and analyzing sequencing BAM/CRAM data

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