jackalope simply and efficiently
simulates (i) haplotypes from reference genomes and (ii) reads from both Illumina
and Pacific Biosciences (PacBio) platforms.
It can either read reference genomes from FASTA files or simulate new ones.
Variant haplotypes 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 reads from Pacific Biosciences
These simulations include sequencing errors, mapping qualities, multiplexing,
and optical/PCR duplicates. All outputs can be written to standard file formats.
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