Rahul Nayak
A Bioinformatician
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GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or...
By Shruti Paniwala 3037 days agoacademic.oup.com - GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap...SIMBA: a Genome Assembly Project Management System
By Neel 2866 days agoufmg-simba.sourceforge.net - SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS)...Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit,...
By Neel 2431 days agowww.phrap.org - Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence...Protocol for De novo Genome Assembly using Illumina Reads
By BioStar 2086 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.Peregrine & SHIMMER Genome Assembly Toolkit
By Abhi 1753 days agogithub.com - Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus. It uses Sparse HIereachical MimiMizER (SHIMMER)...CLAW: Chloroplast Long-read Assembly Workflow
By LEGE 956 days agogithub.com - CLAW (Chloroplast Long-read Assembly Workflow) is an mostly-automated Snakemake-based workflow for the assembly of chloroplast genomes. CLAW uses chloroplast long-reads, which are baited out of larger read libraries (e.g., an Oxford Nanopore...SRF Vacancy at NIPGR
Applications are invited from suitable candidates for filling up the purely temporary position of one Senior Research Fellow in DST’s Indo-Australian Joint project (with ICRISAT) entitled “Genomic Approach for Stress Tolerant Chickpea” under the...GRIDSS: the Genomic Rearrangement IDentification Software Suite
By Rahul Nayak 2331 days agogithub.com - GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants...PeGAS: A Comprehensive Bioinformatic Solution for Pathogenic Bacterial Genomic Analysis
By LEGE 398 days agogithub.com - This is PeGAS, a powerful bioinformatic tool designed for the seamless quality control, assembly, and annotation of Illumina paired-end reads specific to pathogenic bacteria. This tool integrates state-of-the-art open-source software to provide a...SVfinder: Tool for detecting genomic rearrangement form DNA-seq data
By Robert M Willioms 3216 days agogithub.com - SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.
