Package: jackalope 1.1.5

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.

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

jackalope_1.1.5.tar.gz
jackalope_1.1.5.zip(r-4.5)jackalope_1.1.5.zip(r-4.4)jackalope_1.1.5.zip(r-4.3)
jackalope_1.1.5.tgz(r-4.4-x86_64)jackalope_1.1.5.tgz(r-4.4-arm64)jackalope_1.1.5.tgz(r-4.3-x86_64)jackalope_1.1.5.tgz(r-4.3-arm64)
jackalope_1.1.5.tar.gz(r-4.5-noble)jackalope_1.1.5.tar.gz(r-4.4-noble)
jackalope.pdf |jackalope.html
jackalope/json (API)
NEWS

# Install 'jackalope' in R:
install.packages('jackalope', repos = c('https://lucasnell.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lucasnell/jackalope/issues

Uses libs:
  • zlib– Compression library
  • openblas– Optimized BLAS
  • curl– Easy-to-use client-side URL transfer library
  • bzip2– High-quality block-sorting file compressor library
  • xz-utils– XZ-format compression library
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

5.28 score 8 stars 24 scripts 784 downloads 24 exports 10 dependencies

Last updated 11 months agofrom:83688e1e07. Checks:OK: 3 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 02 2024
R-4.5-win-x86_64OKNov 02 2024
R-4.5-linux-x86_64OKNov 02 2024
R-4.4-win-x86_64NOTENov 02 2024
R-4.4-mac-x86_64NOTENov 02 2024
R-4.4-mac-aarch64NOTENov 02 2024
R-4.3-win-x86_64NOTENov 02 2024
R-4.3-mac-x86_64NOTENov 02 2024
R-4.3-mac-aarch64NOTENov 02 2024

Exports:create_genomecreate_haplotypeshaplotypeshaps_gtreeshaps_phylohaps_ssiteshaps_thetahaps_vcfilluminaindelspacbioread_fastaref_genomesub_F81sub_F84sub_GTRsub_HKY85sub_JC69sub_K80sub_TN93sub_UNRESTwrite_fastawrite_gtreeswrite_vcf

Dependencies:apedigestlatticenlmeR6RcppRcppArmadilloRcppProgressRhtslibzlibbioc

Intro to jackalope

Rendered fromjackalope-intro.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2023-11-28
Started: 2019-05-24

Models of nucleotide substitution

Rendered fromsub-models.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2020-02-28
Started: 2018-09-18