Offers a platform dedicated to DNA next-generation sequencing (NGS) data analysis, annotation and visualization. DNAscan can be set for running on various mode to adapt its performance to focus on a specific subregion or material. The application is able to detect a wide range of genetic material including single nucleotides variants (SNVs), repeat expansions and structural variants (SVs). The application can be run through Docker and Singularity.
Allows users to analyze molecular sequences. The Phylemon interface can be used by experts and non-expert users. It contains several types of features: (1) it allows users to design and save phylogenetic pipelines to be used over multiple genes; (2) it makes possible evolutionary analyses, format conversion, file storage and edition of results; and (3) it suggests further analyses, thereby guiding the users through the web server.
Allows construction of matrices for phylogenomic analyses. Agalma is an automated phylogenomics workflow that conducts complete phylogenomic analyses, from raw sequence reads to preliminary phylogenetic trees, with a small number of high-level commands. The software enables fully reproducible phylogenomic studies. The method called treeinform, which uses phylogenetic information to identify misassigned transcripts and reassign them to the same gene, is included in the software.
Performs phylogenetics analyses on trees and sequences. phyx provides a collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects (alignments, trees and Markov Chain Monte Carlo (MCMC) logs). Modelled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams that can be piped to quickly and easily form complex analytical pipelines. Because of the stream-centric paradigm, memory requirements are minimized (often only a single tree or sequence in memory at any instance), and hence phyx is capable of efficiently processing very large datasets.
An easy way for ecologists to make realistic, tenable phylogenies. With phyloGenerator, you can download real DNA sequence data for your species of interest, and then generate a calibrated phylogeny using a defensible constraint tree. Your phylogeny may not be 'correct', but it will have branch lengths based on DNA data and its topology will be safe. It'll be a 'real' phylogeny, not a best-guess from taxonomy filled with polytomies. You don't need to have an advanced knowledge of phylogenetics to use phyloGenerator. Just download the program, follow the guide, and you can build a phylogeny in minutes.
A Python package designed to deliver reproducible phylogenomic analyses. ReproPhylo promotes reproducibility on two levels. First, it eases the complex phylogenomic pipeline design process by providing a simple and concise scripting syntax for the execution of complex and forked phylogenetic workflows. Second, it automates reproducibility by employing well trusted containerization, versioning and provenance programs. In ReproPhylo, management of the experiment’s reproducibility and version control is carried out in a ‘frictionless’ manner in the background, without a need for user attention (although users have the option to access and tailor these aspects). Third, it ensures persistence and availability of metadata throughout the workflow, and in all the final products.
A software package to leverage the utility of the interactive exploratory tools offered by ARB with the computational throughput of cloud-based resources. Arb Tree Generation pipeline serves as middleware between the desktop and the cloud allowing researchers to form local custom databases containing sequences and metadata from multiple resources and a method for linking data outsourced for computation back to the local database.
Produces multiple alignments and trees from genomic data. Hal is a phylogenetic pipeline. The alignments can be produced by a choice of four alignment programs and analyzed by a variety of phylogenetic programs. The Hal pipeline connects the programs BLASTP, MCL, user specified alignment programs, GBlocks, ProtTest and user specified phylogenetic programs to produce species trees.
Tracks evolution from sequence and serological data. Augur is an informatic processing pipeline that aims to subsamples, cleans, aligns sequences and build a phylogenetic tree from this data. The nextstrain project derives from nextflu, which was specific to influenza evolution. nextstrain is comprised of three components: (i) fauna, a database and IO scripts for sequence and serological data, (ii) augur, informatic pipelines to conduct inferences from raw data, and (iii) auspice, a web app to visualize resulting inferences.
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/).