A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator
Create a reference genome.
Create haplotypes from a reference genome.
An R6 Class Representing Haploid Variants
Organize higher-level information for creating haplotypes.
Organize information to create haplotypes using gene trees
Organize information to create haplotypes using phylogenetic tree(s)
Organize information to create haplotypes using segregating sites matr...
Organize information to create haplotypes using theta parameter
Organize information to create haplotypes using a VCF file
Create and write Illumina reads to FASTQ file(s).
Insertions and deletions (indels) specification
jackalope: A Swift, Versatile Phylogenomic and High-Throughput Sequenc...
Create and write PacBio reads to FASTQ file(s).
Read a fasta file.
R6 Class Representing a Reference Genome
Construct necessary information for substitution models.
Write a ref_genome or haplotypes object to a FASTA file.
Write haplotype info from a haplotypes object to a VCF file.
Simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina <https://www.illumina.com/> and Pacific Biosciences (PacBio) <https://www.pacb.com/> platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. 'jackalope' can simulate single, paired-end, or mate-pair Illumina reads, as well as PacBio reads. These simulations include sequencing errors, mapping qualities, multiplexing, and optical/polymerase chain reaction (PCR) duplicates. Simulating Illumina sequencing is based on ART by Huang et al. (2012) <doi:10.1093/bioinformatics/btr708>. PacBio sequencing simulation is based on SimLoRD by Stöcker et al. (2016) <doi:10.1093/bioinformatics/btw286>. All outputs can be written to standard file formats.