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Scrm: efficiently simulating long sequences using the approximated coalescent with recombination.

ABSTRACT:

Motivation

Coalescent-based simulation software for genomic sequences allows the efficient in silico generation of short- and medium-sized genetic sequences. However, the simulation of genome-size datasets as produced by next-generation sequencing is currently only possible using fairly crude approximations.

Results

We present the sequential coalescent with recombination model (SCRM), a new method that efficiently and accurately approximates the coalescent with recombination, closing the gap between current approximations and the exact model. We present an efficient implementation and show that it can simulate genomic-scale datasets with an essentially correct linkage structure.

SUBMITTER: Staab PR

PROVIDER: S-EPMC4426833 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature

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scrm: efficiently simulating long sequences using the approximated coalescent with recombination.

Staab Paul R PR Zhu Sha S Metzler Dirk D Lunter Gerton G

Bioinformatics (Oxford, England) 20150108 10

<h4>Motivation</h4>Coalescent-based simulation software for genomic sequences allows the efficient in silico generation of short- and medium-sized genetic sequences. However, the simulation of genome-size datasets as produced by next-generation sequencing is currently only possible using fairly crude approximations.<h4>Results</h4>We present the sequential coalescent with recombination model (SCRM), a new method that efficiently and accurately approximates the coalescent with recombination, clos ...[more]

PMID: 25596205

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