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1 - 11 of 11 results

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A computer program that conducts targeted local assembly of structural variants (SV) using targeted iterative graph routing assembly algorithm. Using data from the 1000 Genomes Project, TIGRA was able to accurately assemble the majority of deletion and mobile element insertion breakpoints, with a substantively better success rate and accuracy than other algorithms.

MITObim / MITOchondrial Baiting and Iterative Mapping

An in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data-mitochondrial baiting and iterative mapping. MITObim is capable of reconstructing mitochondrial genomes without the need of a reference genome of the targeted species by relying solely on (a) mitochondrial genome information of more distantly related taxa or (b) short mitochondrial barcoding sequences (seeds), such as the commonly used cytochrome-oxidase subunit 1 (COI), as a starting reference.MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24h using a standard desktop computer.

Uses synteny between matching sequences in a target assembly and a reference assembly to layout the contigs (or scaffolds) in the target assembly. The underlying algorithm is based on maximum weight matching. OSLay provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure.

Uses thousands of transcript sequences concurrently to inform the localized assembly of corresponding gene loci. Kollector reconstructs introns and novel sequences within these loci, and scales well to large genomes – properties that makes it especially useful for researchers working on non-model eukaryotic organisms. It successfully reconstructs respectively 99% and 80% (compared to 86% and 73% with standard de novo assembly techniques) of C. elegans and H. sapiens transcript targets in their corresponding genomic space using whole genome shot-gun (WGS) sequencing reads. The tool outperforms both established and recently released targeted assembly tools.

GRAbB / Genome Region Assembly by Baiting

Assembles specific genomic regions from next-generation sequencing (NGS) data. GRAbB is a program using a reference file to identify reads corresponding to the target region. The software is designed to be flexible in terms of input options, assembly and completion criteria. It can handle multiple regions separately within a single run, and is also able to extract homologous sequence regions, such as barcoding sites. GRAbB can serve for extracting specific loci from NGS data, based on homology.

VirusTAP / Virus genome-Targeted Assembly Pipeline

Assembles virus genomes from next generation sequencing (NGS) reads. VirusTAP is a web based platforms for the viral genome that performs the following informatics steps: (i) quality trimming and adaptor removal, (ii) read subtraction of host- and bacteria-related sequences by a read-mapping method, and (iii) de novo assembly using multiple combinations of recently advanced assemblers. It performs simple assembly using idba program.

TASR / Targeted Assembler of [short] Sequence Reads

A genomics application that allows hypothesis-based interrogation of genomic regions (sequence targets) of interest. It only considers NGS reads for assembly that have overlap potential to input sequence targets.

Processes large datasets of reads on commodity hardware. Mapsembler checks the presence of a known piece of information with a bounded number of substitutions in a set of reads. It provides pieces of information about the starter context(s), neighborhoods of approximate occurrences of a starter on some hundreds or thousands of nucleotides. The tool provides features like sub-starters retrieval, iterative extensions and graph visualization.

aTRAM / automated Target Restricted Assembly Method

Assembles genes using a single paired-end genomic library from divergent taxa assembles genes of interest. aTRAM is a software package inspired by the Target Restricted Assembly Method (TRAM). The software assembles genes of interest from short paired-end sequencing reads, including across divergent taxa by iteratively querying and assembling reads. It was used for assembling genes from highly divergent taxa from P. humanus.

PRICE / Paired-Read Iterative Contig Extension

A software for the targeted de novo assembly of genomic sequence from large-scale genomic or metagenomic datasets. PRICE is designed with paired-end data in mind but does not require such data. The features of the underlying software system can be used through two executables: 1) the full assembler, PriceTI, or 2) an executable for independently filtering read data prior to assembly, PriceSeqFilter.

Allows targeted de novo assembly and variance calling. NOVOLoci is a de novo local assembler that enables assembling of regions around set of genes or markers. The software can create a VCF file with all the detected variances, on condition that a reference is available.

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1 - 6 of 6 results

1 - 6 of 6 results

Big data scientist National Institute of Plant Genome Research

Research Interests 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/).

FusionFinder comrad

Mahantesh Biradar

‎Graduate PhD researcher focusing on Cardiovascular Epidemiology & Social Media Enthusiast Research Stash

I'm a Graduate PhD researcher in the area of Biomedical Science and focussing on the Pharmacogenomics/Pharmacogenomics of Diabetes and related complications

Bioinformatician / Genomics scientist

CLC bio NOVOLoci VCF-Explorer

bioinformatician

proovread MITObim SpeedSeq

Richard Winegar

Biosurveillance MRIGlobal

Harvest EbolaVCR VirusTAP

Computational Genomics Stazione Zoologica Anton Dohrn

VirusFinder SID Mobster

Targeted de novo assembly software tools | De novo sequencing data analysis

Production of high quality reference genome sequences for non-model organisms remains a challenging undertaking, especially for large (>1 Gbp) genomes. For such projects, de novo whole-genome assembly typically requires billions of sequencing reads from several different types of DNA libraries. An attractive alternative for generating reference sequences can be achieved through targeted assembly of gene/transcript sequences of interest. Even for species with scant transcriptomic sequence information, there are likely existing sequences that could be used to aid de novo assembly, such as homologous gene sequences from a related organism.

Source text:
(Kucuk et al., 2017) Kollector: transcript-informed, targeted de novo assembly of gene loci. Bioinformatics.

Parent categories

De novo sequencing analysis Rep-seq analysis

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