mitty 2.29.0

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.

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.