jackalope: A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator

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.

Version: 1.0.0
Depends: R (≥ 2.10)
Imports: ape, R6, Rcpp (≥ 0.12.11), zlibbioc
LinkingTo: Rcpp, RcppArmadillo, RcppProgress, Rhtslib, zlibbioc
Suggests: coala, knitr, scrm, testthat
Published: 2019-11-22
Author: Lucas A. Nell ORCID iD [cph, aut, cre]
Maintainer: Lucas A. Nell <lucas at lucasnell.com>
BugReports: https://github.com/lucasnell/jackalope/issues
License: MIT + file LICENSE
URL: https://github.com/lucasnell/jackalope
NeedsCompilation: yes
SystemRequirements: GNU make, C++11
Citation: jackalope citation info
Materials: README NEWS
CRAN checks: jackalope results

Downloads:

Reference manual: jackalope.pdf
Vignettes: Intro to jackalope
Models of nucleotide substitution
Package source: jackalope_1.0.0.tar.gz
Windows binaries: r-devel: jackalope_1.0.0.zip, r-devel-gcc8: jackalope_1.0.0.zip, r-release: jackalope_1.0.0.zip, r-oldrel: jackalope_1.0.0.zip
OS X binaries: r-release: jackalope_1.0.0.tgz, r-oldrel: not available
Old sources: jackalope archive

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