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SUMMARY: There is an immediate need for tools to both analyse and visualize in real-time single-nucleotide polymorphisms, insertions and deletions, and other structural variants from new sequence file formats. We have developed VarB software that can be used to visualize variant call format files in real time, as well as identify regions under balancing selection and informative markers to differentiate user-defined groups (e.g. populations). We demonstrate its utility using sequence data from 50 Plasmodium falciparum isolates comprising two different continents and confirm known signals from genomic regions that contain important antigenic and anti-malarial drug-resistance genes. AVAILABILITY AND IMPLEMENTATION: The C++-based software VarB and user manual are available from www.pathogenseq.org/varb. CONTACT: taane.clark@lshtm.ac.uk

Original publication

DOI

10.1093/bioinformatics/bts557

Type

Journal article

Journal

Bioinformatics

Publication Date

15/11/2012

Volume

28

Pages

2983 - 2985

Keywords

Genetic Variation, Genome, Protozoan, High-Throughput Nucleotide Sequencing, INDEL Mutation, Plasmodium falciparum, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Software