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bioconda/mitosalt

mitosalt

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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.

Installation

To install this package, run one of the following:

Conda
$conda install bioconda::mitosalt

Usage Tracking

1.1.1
1 / 8 versions selected
Downloads (Last 6 months): 0

Description

This mitosalt version can:

  • download 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]
  • let us choose the destination folder of the reference genomes and indices
    • export MITOSALTDATA=/path/to/mitosalt/genomedata
  • specify custom config files that are available in the package at $CONDA_PREFIX/share/mitosalt-1.1.1-0/

About

Summary

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.

Last Updated

Feb 27, 2025 at 20:12

License

MIT-0

Total Downloads

444

Supported Platforms

noarch

Home

https://sourceforge.net/projects/mitosalt/