jackalope

jackalope simulates high-throughput sequencing reads and genomic variants to support population genomics and phylogenomics study design.

Key Features:

• Versatile Variant Simulation: Simulates genomic variants from reference genomes using phylogenies, gene trees, coalescent-simulation outputs, population-genomic summary statistics, or Variant Call Format (VCF) files.
• Platform-Specific Read Simulation: Generates Illumina (single-end, paired-end, and mate-pair) and Pacific Biosciences (PacBio) reads while modeling sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates.
• Reference Genome Handling: Reads reference genomes from FASTA files and can simulate new reference genomes.
• Standard Output Formats: Produces outputs compatible with standard bioinformatics file formats.

Scientific Applications:

• Population Genomics: Designs and assesses sequencing strategies, coverage requirements, and variant-calling performance under complex evolutionary scenarios.
• Phylogenomics: Simulates sequence evolution along phylogenies and gene trees to evaluate phylogenetic inference methods.
• Benchmarking and Validation: Generates realistic HTS datasets with sequencing artifacts to benchmark variant-calling pipelines and other bioinformatic tools.

Methodology:

Reads reference genomes from FASTA files and simulates genomic variants and sequencing reads using algorithms that incorporate evolutionary models and sequencing artifacts.