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jackalope: A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator
Description
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) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/btr708")}. PacBio sequencing simulation is based on SimLoRD by Stöcker et al. (2016) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/btw286")}. All outputs can be written to standard file formats.
Author(s)
Maintainer: Lucas A. Nell lucnell@gmail.com (ORCID) [copyright holder]
See Also
Useful links:
jackalope documentation built on May 29, 2024, 3:58 a.m.
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| jackalope-package | R Documentation |
jackalope: A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator
Description
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) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/btr708")}. PacBio sequencing simulation is based on SimLoRD by Stöcker et al. (2016) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/btw286")}. All outputs can be written to standard file formats.
Author(s)
Maintainer: Lucas A. Nell lucnell@gmail.com (ORCID) [copyright holder]
See Also
Useful links:
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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