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Bioinformatics. 2015 May 15;31(10):1680-2. doi: 10.1093/bioinformatics/btu861. Epub 2015 Jan 8.

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

Author information

1
Department of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.

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.

PMID:
25596205
PMCID:
PMC4426833
DOI:
10.1093/bioinformatics/btu861
[Indexed for MEDLINE]
Free PMC Article

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