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 simulationsâthe 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: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=jackalope to link to this page.
RetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4