A tool designed to provide clinically relevant information distributed in disparate resources for understanding and annotating human mitochondrial DNA variations. The pipeline has two components: a command-line component that provides automation for alignment of NGS reads to the modified rCRS; and an online version that provides a comprehensive genetic report of mitochondrial variants, which includes information about the corresponding mutation, gene, associated phenotype and population frequency. mit-o-matic also reports the estimated haplogroup, disease associated variations and heteroplasmic sites.
An effective workflow with customizable parameters and able to analyze multiple samples in a single run. MToolBox is the only tool that generates as output a VCF file, the standard format for large-scale genotyping information, suitably customized for mitochondrial data, by including the heteroplasmy fraction and its related confidence interval. Additionally, MToolBox provides the user with essential analyses of reconstructed mitochondrial genomes, i.e. haplogroup assignment and variant prioritization, exploiting a broad collection of annotation resources. Thus, MToolBox may provide a valuable support for the recognition of candidate mitochondrial mutations in clinical studies.
Conducts analysis for human mitochondrial DNA (mtDNA) next generation sequencing (NGS) data. mtDNA-Server is useful for the discovery of heteroplasmic sites, contamination determination and numerous quality control (QC) statistics. It can serve for the evaluation of data from whole genome sequencing investigations for potential contamination and is therefore not limited to target mtDNA sequencing.
An open-source software tool that can reliably and easily extract mitochondrial genome information from exome and whole genome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers and detects heteroplasmy, somatic mutation and structural variants of the mitochondrial genome. MitoSeek can be set up to run in parallel or serial on large exome sequencing datasets.
Estimates Mitochondrial DNA (mtDNA) copy number highly accurately using 0.1% of the genome. fastMitoCalc is an application that takes advantage of the indexing of sequencing alignment files, focusing on a small subset of the nuclear genome to estimate autosomal DNA coverage accurately. It analyzes hundreds of thousands of genomes currently being sequenced by large research consortia, and facilitates association studies of mtDNA copy number with quantitative trait values or nuclear variants.
Provides a web service for standardized mtDNA variant annotations. mvTool is available through a web application and incorporates user-friendly input and output format options. It includes (i) a converter that supports all classical mtDNA variant nomenclature and (ii) an annotator module pools population frequency data about mtDNA variants from multiple sources and provides over 100 types of in silico annotations and predictions.
Extracts mitochondrial DNA from whole genome sequencing (WGS) data. Norgal is an assembly method that allows extraction and assembly full or partial mitochondrial and chloroplast genomes from WGS short reads, especially in situations where reference sequences are unavailable. The mitochondrial genome of the Oriental hornet (Vespa orientalis) was published using a Norgal assembly. The software thus contributes to the field of discovering and assembling novel mitochondrial sequences from WGS data.
Allows users to analyze, annotate and report human mitochondrial DNA variants from next-generation sequencing (NGS) data. SG-ADVISER mtDNA is a web server built on top of MToolBox, an automated bioinformatics pipeline. The software aims to simplify calling, annotation and interpretation of human mitochondrial DNA (mtDNA) variants. 200 unpublished mtDNA genomes from a healthy aging cohort were used to test the software.
Allows users to analyze data from high-throughput sequencing (HTS) of the human mitochondrial genome. MitoSuite is a graphical tool that supports quality check of alignment data, variant annotation, building consensus sequences, haplogroup classification, and detection of heteroplasmic sites, exogenous contamination, and base-substitution patterns for mitochondrial genome data obtained by HTS. The software is especially designed for non-bioinformaticians unfamiliar with typing complicated commands.
Allows users to choose the ontogenetic processes to place in the ontogenetic phylogeny. mope is an useful solution to study the dynamics of cancer evolution, or heterogeneous progression in samples of many tumors. It also can be used in the typical population phylogenetic setting to infer the divergence history of a group of populations.
A simple web-based tool for analyzing heteroplasmy using sequences generated by second generation sequencing technology, specifically designed for studying the functional potential of mtDNA heteroplasmy in humans. MitoBamAnnotator receives files describing the alignment of mtDNA next generation sequences to the mtDNA genome or a list of mutated positions as input, and provides a richly annotated report of suspected heteroplasmic sites. Users control the filtration process by modifying the filtration parameters, and receive the results in a compact table which can be further filtered using spreadsheet editing programs such as Microsoft Excel or open-access equivalents.
Gene fusion detection in Plants
Fusion transcripts (i.e., chimeric RNAs) resulting from gene fusions are well known in case of human. But, in plants, this phenomenon is not yet explored. We are planning to discover the fusion transcripts/gene fusions in different type of plants by using RNA-Seq datasets. Further, we are planning to understand the mechanism of gene fusion formation and significance of fusions in plants.
Whole genome and transcriptome sequencing data analysis of Plants
In this era of Next Generation Sequencing (NGS), there is huge amount of sequencing data available in the public domain. Any novel finding from these available datasets is major challenge for a computational biologist. We are interested in the analysis of whole genome and transcriptome sequencing data of different plants to fetch out the useful information from those datasets, with the help of bioinformatics tools. Currently, we are planning to study the gene clusters of secondary metabolite pathways in different plants.
Development of webservers, databases and computational pipelines for plant research
Development of database is necessary to compile and share the information with scientific community. We are dedicated to develop useful databases and webserver for plant research.
Another area of interest is to develop automated pipelines and tools for the analysis of high throughput genomics data, generated by NGS technologies.
Professional & Academic Background
Staff Scientist II (May 2017- present): National Institute of Plant Genome Research (NIPGR), New Delhi, India
Postdoctoral Research Associate (2015-2017): University Of Virginia, Charlottesville, VA, USA
Research Scientist (2014-2015): Sir Ganga Ram Hospital, New Delhi, India
PhD Bioinformatics (2009-2014): Bioinformatics Centre, Institute of Microbial Technology (IMTECH), Chandigarh under Jawaharlal Nehru University (JNU), New Delhi, India
M.Sc. Life Sciences (2007-2009): Jawaharlal Nehru University (JNU), New Delhi, India
B.Sc. Biotechnology (2004-2007): Jamia Millia Islamia (JMI), New Delhi, India
Awards and Fellowships
Junior and Senior Research Fellowship (2009-2014): Council of Scientific and Industrial Research (CSIR), New Delhi, India
GATE (Graduate Aptitude Test in Engineering): Qualified in years 2008 and 2009
Scientific Contributions/ Recognitions
Associate editor: Journal of Translational Medicine.
Editorial Board Member of Journal: Theoretical Biology and Medical Modelling.
Reviewer: PloS One, BMC Genomics, BMC Bioinformatics, BMC Biology, BMC Biotechnology, Frontiers in Physiology and several other journals.
Web Resources/ Databases (Developed/ Contributed)
A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer (http://www.imtech.res.in/raghava/cancertope/)
GenomeABC: A webserver for benchmarking of genome assemblers. (http://crdd.osdd.net/raghava/genomeabc/).
Genomics web portal page. (http://crdd.osdd.net/raghava/genomesrs/).
Map/Alignment module of CancerDr: Cancer Drug Resistance Database. (http://crdd.osdd.net/raghava/cancerdr/).
Short reads and contigs alignment module of PCMDB: Pancreatic cancer methylation database. (http://crdd.osdd.net/raghava/pcmdb/).
Burkholderia sp. SJ98 database. (http://crdd.osdd.net/raghava/genomesrs/burkholderia/).
Rhodococcus imtechensis RKJ300 database. (http://crdd.osdd.net/raghava/genomesrs/rkj300/).
Genotrick: A pipeline for whole genome assembly and annotation of Genomes (http://crdd.osdd.net/raghava/genomesrs/genotrick/)
Development of Debian packages in OSDDlinux: A Customized Operating System for Drug Discovery. (http://osddlinux.osdd.net/).
A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. (http://crdd.osdd.net/raghava/mtbveb/).