Simulator for genomic data
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.
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