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

Abstract

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. Availability and implementation: The open source implementation scrm is freely available at https://scrm.github.io under the conditions of the GPLv3 license. Contact: staab@bio.lmu.de or gerton.lunter@well.ox.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.