title: tbvar: A comprehensive genome variation resource for Mycobacterium tuberculosis.
abstract: Mycobacterium tuberculosis, along with closely related species, commonly known as M. tuberculosis complex (MTBC), causes tuberculosis in humans and other organisms. Tuberculosis is a disease with high morbidity and mortality, especially in the third world. The genetic variability between clinical isolates of MTBC has been poorly understood, although recent years have seen the re-sequencing of a large number of clinical isolates of MTBC from around the world. The availability of genomic data of multiple isolates in public domain would potentially offer a unique opportunity toward understanding the variome of the organism and the functional consequences of the variations. This nevertheless has been limited by the lack of systematic curation and analysis of data sets available in public domain. In this report, we have re-analyzed re-sequencing data sets corresponding to >450 isolates of MTBC available in public domain to create a comprehensive variome map of MTBC comprising >29 000 single nucleotide variations. Using a systematic computational pipeline, we have annotated potential functional variants and drug-resistance-associated variants from the variome. We have made available this data set as a searchable database. Apart from a user-friendly interface, the database also has a novel option to annotate variants from clinical re-sequencing data sets of MTBC. To the best of our knowledge, tbvar is the largest and most comprehensive genome variation resources for MTBC. Database URL: http://genome.igib.res.in/tbvar/
authors.affiliation: CSIR Open Source Drug Discovery Unit, Anusandhan Bhawan, Delhi 110001, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Delhi 110001, India; Department of Biotechnology, Delhi Technological University, Bawana Road, Delhi 110042, India and GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India.
authors.forename: Kandarp Rakeshkumar
authors.initials: KR
authors.lastname: Joshi
authors.forename: Heena
authors.initials: H
authors.lastname: Dhiman
authors.forename: Vinod
authors.initials: V
authors.lastname: Scaria
mesh_terms: D030541:Databases, Genetic; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation; D009169:Mycobacterium tuberculosis / Q000235:genetics*; D012984:Software; D013223:Statistics as Topic