title: scrm: efficiently simulating long sequences using the approximated coalescent with recombination.
abstract: BACKGROUND
  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.
authors.affiliation: Department of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
authors.forename: Paul R
authors.initials: PR
authors.lastname: Staab
authors.affiliation: Department of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
authors.forename: Sha
authors.initials: S
authors.lastname: Zhu
authors.affiliation: Department of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
authors.forename: Dirk
authors.initials: D
authors.lastname: Metzler
authors.affiliation: Department of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
authors.forename: Gerton
authors.initials: G
authors.lastname: Lunter
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008040:Genetic Linkage; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008957:Models, Genetic; D011995:Recombination, Genetic; D012984:Software