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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.

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