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bfxcss / packages / mitosalt 1.1.1

MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided.

Installers

  • noarch v1.1.1

conda install

To install this package run one of the following:
conda install bfxcss::mitosalt

Description

This is a patched version of mitosalt that includes:

  • a fix for the setup script to allow for installation in a conda environment
  • a fix for the download of user-selected reference genomes
    • download-mitosalt-db.sh -h [human_genome_url, blank for custom hg19 genome]
    • download-mitosalt-db.sh -m [mouse_genome_url, blank for custom GRCm38.p6 genome]
    • download-mitosalt-db.sh -h [human_genome_url, blank for custom hg19 genome] -m [mouse_genome_url, blank for custom GRCm38.p6 genome]
  • a fix for choosing the destination folder of the reference genomes and indices
    • export MITOSALTDATA=/path/to/mitosalt/genomedata
  • custom config files available in the package at $CONDA_PREFIX/share/mitosalt-1.1.1-0/
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