jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• High-throughput sequencing (HTS) is crucial for population genomics and phylogenetics.
• Research design choices in HTS projects involve sequencing platforms, coverage depth, and bioinformatics tools.
• Current HTS simulators lack the ability to generate variant haplotypes under complex evolutionary scenarios like recombination or demographic changes, limiting their utility.

Purpose of the Study:

• To present the R package jackalope for simulating HTS data.
• To enable simulation of variant haplotypes and sequencing reads from various evolutionary scenarios.
• To provide a tool that aids in research design and software validation for population genomics and phylogenomics.

Main Methods:

• The jackalope R package simulates variant haplotypes from a reference genome.
• It simulates sequencing reads for Illumina (single, paired-end, mate-pair) and Pacific Biosciences platforms.
• Simulations incorporate evolutionary scenarios (phylogenies, gene trees, coalescent output, VCF files) and sequencing artifacts (errors, duplicates, multiplexing).

Main Results:

• jackalope efficiently simulates variant haplotypes and sequencing reads.
• The package supports diverse evolutionary models and input data formats (VCF, FASTA).
• Simulated reads accurately reflect real-world sequencing complexities including errors and duplicates.

Conclusions:

• jackalope enhances the utility of HTS data simulation for population genomics and phylogenomics.
• The package provides a flexible and efficient tool for generating realistic HTS data, aiding research design and software validation.
• jackalope is available for Mac, Windows, and Linux systems.