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
Suggests: coala, knitr, markdown, rmarkdown, scrm, testthat
VignetteBuilder: knitr
URL: https://github.com/lucasnell/jackalope
BugReports: https://github.com/lucasnell/jackalope/issues
NeedsCompilation: yes
Packaged: 2025-09-29 20:28:48 UTC; lucasnell
Author: Lucas A. Nell [cph, aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3209-0517>)
Maintainer: Lucas A. Nell <lucnell@gmail.com>
Repository: CRAN
Date/Publication: 2025-09-29 21:00:02 UTC
Built: R 4.6.0; aarch64-apple-darwin23; 2026-04-26 01:00:21 UTC; unix
Archs: jackalope.so.dSYM
