File editing bioinformatics tools | Next-generation sequencing analysis - OMICtools

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Permits to create, parse, edit and write graphical fragment assembly (GFA) files. GfaPy provides a complete interface to parse files in GFA, a format allowing for the description of generic sequence graphs. It can be modified to incorporate future changes in the GFA specification. It offers syntactic and semantic validation to guarantee valid GFA data. It can be used for GFA 1 and GFA 2 files.

Allows researchers to manipulate CSV and TSV files. csvtk is based on the utilization of shell commands and permits rapid data investigation. It can be implemented into analysis pipelines.

Groups several programs assisting users to work on SAM/BAM files. For using BamUtil, users have to download the libStatGen program.

Provides string containers, string matching algorithms, and utilities for manipulating large biological sequences or sets of sequences. Biostrings is an R package that uses (1) R external pointers to store the string data, (2) bit patterns to encode the string data, and (3) provides users with a class of objects where each instance can store a set of views on the same big string.

Replaces or deletes sequence sections. biosed is a simple sequence editing utility that searches for a target subsequence in one or more input sequences and replaces it with an insert subsequence, or optionally, just deletes the target subsequence where found. If the target subsequence occurs more than once, then each instance of the target is replaced or deleted. The -position option allows a sequence position to be specified as an additional constraint for the match: a replacement/deletion only occurs if the start of a match is at the specified -position position.

Offers to users several features to exploit genes and transcripts in general feature format (GFF) through the gene transfer format (GTF2) and GFF3 versions. GFF utilities provides a tool, gffread, for the validation, filtering and converting GFF files. gffcompare is another program that allows the evaluation and comparison of the accuracy of transcript assemblers and the intron/exon coordinates.

Provides a binary package to read raw signal data from FAST5 files. python-fast5 is a library for accessing Oxford Nanopore Technologies sequencing data. It includes a read-write access to fast5 files and a Python wrapper that enables read-only access to fast5 files.

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Bioinformatician OmicX

PhD ès Neurosciences, I worked 8 years on the brain and its diseases. I then specialized in bioinformatics (NGS, epigenetics) and worked in CEA and GENETHON before to join OMICX and help OMICtools community.

aCNViewer MEDOC Bowtie

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

Bioinformatician Purdue University

Bismark

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

PhD Student Institute of Life Sciences

Working on Immunology and Systems Biology.

EuMicrobedbLite Bowtie GATK

INSERM U1065, C3M University of Nice Sophia-Antipolis, France French Institute of Health and Medical Research

PIPE-chipSAD

Rodrigo Bacigalupe

Scientist Flanders Institute for Biotechnology

Antoine Rousselin

Ingénieur d'étude Centre Franois Baclesse

ONCOCNV CNVkit CNV-seq

olga Adame Guerero

Student Universidad Autónoma de Guerrero