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: | 1.1.5 |
| Depends: | R (≥ 2.10) |
| Imports: | ape, R6, Rcpp (≥ 0.12.11), zlibbioc |
| LinkingTo: | Rcpp, RcppArmadillo, RcppProgress, Rhtslib, zlibbioc |
| Suggests: | coala, knitr, markdown, rmarkdown, scrm, testthat |
| Published: | 2023-11-28 |
| DOI: | 10.32614/CRAN.package.jackalope |
| Author: | Lucas A. Nell 
[cph, aut, cre] |
| Maintainer: | Lucas A. Nell <lucnell at gmail.com> |
| BugReports: | https://github.com/lucasnell/jackalope/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/lucasnell/jackalope |
| NeedsCompilation: | yes |
| SystemRequirements: | GNU make |
| Citation: | jackalope citation info |
| Materials: | README NEWS |
| CRAN checks: | jackalope results |
Documentation:
| Reference manual: | jackalope.pdf |
| Vignettes: |
Intro to jackalope Models of nucleotide substitution |
Downloads:
| Package source: | jackalope_1.1.5.tar.gz |
| Windows binaries: | r-devel: jackalope_1.1.5.zip, r-release: jackalope_1.1.5.zip, r-oldrel: jackalope_1.1.5.zip |
| macOS binaries: | r-release (arm64): jackalope_1.1.5.tgz, r-oldrel (arm64): jackalope_1.1.5.tgz, r-release (x86_64): jackalope_1.1.5.tgz, r-oldrel (x86_64): jackalope_1.1.5.tgz |
| Old sources: | jackalope archive |
Linking:
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