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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.

Features

  • 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


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