SAMFIRE: multi-locus variant calling for time-resolved sequence data

Abstract

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/

Contact: chris.illingworth@gen.cam.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Increasing genetic diversity of the V3 loop of HIV envelope protein observed via calling of time-resolved multi-locus haplotypes. Numbered pie charts show the proportion of each haplotype observed from viral data collected from a single patient. The area of a segment in a single chart is proportional to the fraction of sequences observed to have the given multi-locus haplotype at each time. Dotted lines connect multi-locus haplotypes that differ by a single mutation (Color version of this figure is available at Bioinformatics online.)