Skip to main content

Simulator for genomic data

Project description

Mitty is a data simulator meant to help debug aligners and variant callers.

It requires Python 3.4 or later. It is released under the Apache 2.0 license.


  • Generate reads from the whole genome, a single tiny region or from a set of regions as desired

  • Handles X, Y chromosomes and polyploidy IF the VCF GT field is properly set

  • Read qname stores correct POS, CIGAR and the sizes of variants covered by the read

  • Name of sample included in read allowing us to mix FASTQs from different simulations/sources

    • Can mix viral contamination into reads

    • Can do tumor/normal mixes

  • Corruption module adds sequencing errors to reads

    • Read models can be sampled from existing BAM files

  • “God aligner” writes out a BAM with perfect alignments which can be used for BAM comparisons

  • Simple genome simulator to generate VCFs with SNPs and different sizes of Insertions and Deletions for aligner/caller testing

  • Analyze, plot and debug alignment accuracy with composable analysis functions

Tutorial and usage manual can be found here.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

mitty-2.29.0.tar.gz (1.3 MB view hashes)

Uploaded Source

Built Distribution

mitty-2.29.0-py3-none-any.whl (1.3 MB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page