SAMFIRE: multi-locus variant calling for time-resolved sequence data
Oxford University Press
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Illingworth, C. (2016). SAMFIRE: multi-locus variant calling for time-resolved sequence data. Bioinformatics https://doi.org/10.1093/bioinformatics/btw205
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 analysing 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.
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).
Wellcome Trust (101239/Z/13/Z)
External DOI: https://doi.org/10.1093/bioinformatics/btw205
This record's URL: https://www.repository.cam.ac.uk/handle/1810/255804