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) . PacBio sequencing simulation is based on SimLoRD by Stöcker et al. (2016) . All outputs can be written to standard file formats.


Reference manual

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1.1.3 by Lucas A. Nell, 7 months ago


Report a bug at https://github.com/lucasnell/jackalope/issues

Browse source code at https://github.com/cran/jackalope

Authors: Lucas A. Nell [cph, aut, cre]

Documentation:   PDF Manual  

MIT + file LICENSE license

Imports ape, R6, Rcpp, zlibbioc

Suggests coala, knitr, markdown, rmarkdown, scrm, testthat

Linking to Rcpp, RcppArmadillo, RcppProgress, Rhtslib, zlibbioc

System requirements: GNU make, C++11

See at CRAN