Illingworth, C.J.R. (2016) SAMFIRE: multi-locus variant calling for time-resolved sequence data. Bioinformatics, 32(14), pp. 2208-2209. (doi: 10.1093/bioinformatics/btw205) (PMID:27153641) (PMCID:PMC4937198)
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Abstract
Summary: An increasingly common method for studying evolution is the collection of time-resolved short-read sequence data. Such datasets allow for the direct observation of rapid evolutionary processes, as might occur in natural microbial populations and in evolutionary experiments. In many circumstances, evolutionary pressure acting upon single variants can cause genomic changes at multiple nearby loci. SAMFIRE is an open-access software package for processing and analyzing sequence reads from time-resolved data, calling important single- and multi-locus variants over time, identifying alleles potentially affected by selection, calculating linkage disequilibrium statistics, performing haplotype reconstruction and exploiting time-resolved information to estimate the extent of uncertainty in reported genomic data. Availability and Implementation: C ++ code may be found at https://github.com/cjri/samfire/.
| Item Type: | Articles |
|---|---|
| Additional Information: | CI was supported by a Sir Henry Dale Fellowship, jointly funded by the Wellcome Trust and the Royal Society (Grant Number 101239/Z/13/Z). |
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Illingworth, Dr Chris |
| Authors: | Illingworth, C.J.R. |
| College/School: | College of Medical Veterinary and Life Sciences > School of Infection & Immunity College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research |
| Journal Name: | Bioinformatics |
| Publisher: | Oxford University Press |
| ISSN: | 1367-4803 |
| ISSN (Online): | 1460-2059 |
| Published Online: | 22 April 2016 |
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