Open Source Drug Discovery (OSDD) genomes of clinical isolates of Mycobacterium tuberculosis from India

Genes and Genomes
The OSDD OpenLab has been maintaining the OSDD Open Access Repository of clinical isolates of Mycobacterium tuberculosis. A number of isolates from this repository has been sequenced and available in public domain.

A number of genomes from the OSDD Open Access Repository has been sequenced in Dr. Sridhar Sivasubbu Laboratory in collaboration. A complete list of the sequenced strains and publications are available here.

TBvar Resource for Genomic Variations
tbvar is a comprehensive resource for genomic variations in Mycobacterium tuberculosis The variations have been systematically retrieved from high-throughput re-sequencing data-sets. In addition, Using a systematic computational pipeline, potential genomic variations with functional consequences and association with drug resistance have been characterized.

Access this resource at URL: http://genome.igib.res.in/tbvar

Joshi KR, Dhiman H, Scaria V*

Funding and Support
We acknowledge the funding from the Open Source Drug Discovery Initiative/ CSIR for the programme. We also acknowledge the availability of communication and compute resources from NKN for the project.
Publications

Periwal V, Patowary A, Vellarikkal SK, Gupta A, Singh M, Mittal A, Jeyapaul S, Chauhan RK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch, K, OSDD Consortium, Chauhan DS*, Sivasubbu S*, Scaria V*
Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome
PLoS ONE (2015)
Apr 8;10(4):e0122979. doi: 10.1371/journal.pone.0122979. eCollection 2015.

Sahajpal R, Kandoi G, Dhiman H, Raj S, OSDD Consortium, Scaria V, Bhartiya D and Hasija Y
HGV&TB: A comprehensive online resource on Human genes and genetic variants associated with Tuberculosis
Database (2014) Dec 13;2014:bau112. doi: 10.1093/database/bau112.

Joshi KR, Dhiman H, Scaria V*

Vellarikkal SK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K; Open Source Drug Discovery Consortium, Chauhan DS, Sivasubbu S, Scaria V.
Draft Genome Sequence of a Multidrug-Resistant Clinical Isolate of Mycobacterium tuberculosis Belonging to a Novel Spoligotype.
Genome Announc. 2013 Nov 21;1(6). pii: e00965-13. doi: 10.1128/genomeA.00965-13.

Vellarikkal SK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K; Open Source Drug Discovery Consortium, Chauhan DS, Sivasubbu S, Scaria V.
Draft Genome Sequence of Multidrug-Resistant Mycobacterium tuberculosis Clinical Isolate OSDD515, Belonging to the Uganda I Genotype.
Genome Announc. 2013 Nov 21;1(6). pii: e00750-13. doi: 10.1128/genomeA.00750-13.

Karuthedath Vellarikkal S, Vir Singh A, Kumar Singh P, Garg P, Mohan Katoch V, Katoch K; Open Source Drug Discovery Consortium, Chauhan DS, Scaria V, Sivasubbu S.
Draft Genome Sequence of an Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate of the Ural Strain OSDD493.
Genome Announc. 2013 Nov 7;1(6). pii: e00928-13. doi: 10.1128/genomeA.00928-13.

Karuthedath Vellarikkal S, Patowary A, Singh M, Periwal V, Singh AV, Singh PK, Garg P, Mohan Katoch V, Katoch K, Jangir PK, Sharma R; Open Source Drug Discovery Consortium, Chauhan DS, Scaria V, Sivasubbu S.

Bhardwaj A, Bhartiya D, Kumar N, Open Source Drug Discovery Consortium, Scaria V*
TBrowse: an Integrative Genomics Map of Mycobacterium tuberculosis.
Tuberculosis 2009 Sep;89(5):386-7. doi: 10.1016/j.tube.2009.07.005
Genome Data Accessions

Mycobacterium tuberculosis OSDD493 Accession: PRJNA213484 ID: 213484
Mycobacterium tuberculosis str. OSDD515 Accession: PRJNA213253 ID: 213253
Mycobacterium tuberculosis OSDD105 Accession: PRJNA213252 ID: 213252
Mycobacterium tuberculosis EAI/OSDD271 Accession: PRJNA196573 ID: 196573
Mycobacterium tuberculosis OSDD518 Accession: PRJNA193380 ID: 193380
Mycobacterium tuberculosis OSDD487 Accession: PRJNA193379 ID: 193379
Mycobacterium tuberculosis OSDD326 Accession: PRJNA193378 ID: 193378
Mycobacterium tuberculosis OSDD472 Accession: PRJNA193377 ID: 193377
Mycobacterium tuberculosis OSDD354 Accession: PRJNA193326 ID: 193326
Mycobacterium tuberculosis OSDD500 Accession: PRJNA193323 ID: 193323
Mycobacterium tuberculosis OSDD504 Accession: PRJNA193305 ID: 193305
Mycobacterium tuberculosis OSDD071 Accession: PRJNA193304 ID: 193304
Mycobacterium tuberculosis OSDD630 Accession: PRJNA193298 ID: 193298
Mycobacterium tuberculosis OSDD518 Accession: PRJNA78961 ID: 78961
Mycobacterium tuberculosis OSDD504 Accession: PRJNA78959 ID: 78959
Mycobacterium tuberculosis OSDD071 Accession: PRJNA78807 ID: 78807