Poonam Mahapatra
Bioinformatics Researcher
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ShRec3D
By Jitendra Narayan 3656 days agosites.google.com - ShRec3D is a program that aims at reconstructing a genome 3D structure (b) from the sole knowledge of the contacts between different genomic regions (a) as determined by Hi-C (http://www.ncbi.nlm.nih.gov/pubmed/19815776). There are two options to...gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
By Rahul Nayak 1800 days agogithub.com - gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and...ngs-bits - Short-read sequencing tools
By Neel 1808 days agogithub.com - Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources: Binaries for Linux/macOS From sources for Linux/macOS From sources for WindowsNicolas Corradi Lab
The goal of our research is to better understand the biology of microbial organisms of significant ecological, veterinary and medical importance. To achieve this goal, our team combines the power of next generation DNA sequencing and...Staff Scientists at National Institute of Plant Genome Research, New Delhi
National Institute of Plant Genome Research, New Delhi is an Autonomous Research Institution funded by Department of Biotechnology, Ministry of Science & Technology, Govt. of India, to pursue research on various aspects of plant genomics. The...n50PlottingTools
By Jit 3246 days agogithub.com - Tools to create plots showing N-statistics for genome assemblies More at https://github.com/dentearl/n50PlottingToolsGenome Browser : GBrowse
By Jit 3235 days agoelp.ucdavis.edu - Generic Genome Browser Version 2: A Tutorial for Administrators This is an extensive tutorial to take you through the main features and gotchas of configuring GBrowse as a server. This tutorial assumes that you have successfully set up Perl, GD,...Stacks
By Jitendra Narayan 3230 days agocatchenlab.life.illinois.edu - Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps...RNA-Seq De novo Assembly Using Trinity
By Surabhi Chaudhary 3202 days agogithub.com - Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules:...
