Package: jackalope
Type: Package
Title: A Swift, Versatile Phylogenomic and High-Throughput Sequencing
        Simulator
Version: 1.1.6
Authors@R: person(c("Lucas", "A."), "Nell", email = "lucnell@gmail.com", 
                    role = c("cph", "aut", "cre"),
                    comment = c(ORCID = "0000-0003-3209-0517"))
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
biocViews:
Imports: ape, R6, Rcpp (>= 0.12.11)
LinkingTo: Rcpp, RcppArmadillo, RcppProgress, Rhtslib
SystemRequirements: GNU make
RoxygenNote: 7.3.3
Roxygen: list(markdown = TRUE)
Suggests: coala, knitr, markdown, rmarkdown, scrm, testthat
VignetteBuilder: knitr
URL: https://github.com/lucasnell/jackalope
BugReports: https://github.com/lucasnell/jackalope/issues
Config/pak/sysreqs: make libbz2-dev liblzma-dev xz-utils zlib1g-dev
Repository: https://lucasnell.r-universe.dev
Date/Publication: 2025-09-29 20:30:24 UTC
RemoteUrl: https://github.com/lucasnell/jackalope
RemoteRef: HEAD
RemoteSha: b119c7728dc909e12347dbb2165309756d7cf84f
NeedsCompilation: yes
Packaged: 2026-07-05 03:03:03 UTC; root
Author: Lucas A. Nell [cph, aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3209-0517>)
Maintainer: Lucas A. Nell <lucnell@gmail.com>