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|1.||Bioinformatics. 2012 Sep 13. [Epub ahead of print]|
VarB: A Variation Browsing and analysis tool for variants derived from next-generation sequencing data.Preston MD, Manske M, Horner N, Assefa S, Campino S, Auburn S, Zongo I, Oudraogo JB, Nosten F, Anderson T, Clark TG.
London School of Hygiene and Tropical Medicine, London, UK; Wellcome Trust Sanger Institute (WTSI), Hinxton, UK; Faculty of Health, Cranfield University, Cranfield, Bedfordshire, UK; Institut de Recherche en Sciences de la Sant, Bobo-Dioulasso, Burkina Faso Shoklo Malaria Research Unit, Mae Sot, Thailand; Texas Biomedical Research Institute, San Antonio, Texas, USA.
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 visualise Variant Call Format (VCF) 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 fifty 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: firstname.lastname@example.org or email@example.com.
|PMID: 22976080 [PubMed - as supplied by publisher]|