Rahul Nayak
A Bioinformatician
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Scaffolding of a bacterial genome using MinION nanopore sequencing
By Rahul Agarwal 3438 days agowww.nature.com - Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot...Jvarkit : Java utilities for Bioinformatics
By Jit 2371 days agolindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for BioinformaticsnQuire: a statistical framework for ploidy estimation using next generation sequencing
By Jit 2253 days agogithub.com - nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where...Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Rahul Nayak 2578 days agogithub.com - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq dataAfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good...MIX: Combining multiple assemblies from NGS data
By Rahul Nayak 2402 days agogithub.com - Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices...NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
By Jit 2312 days agogithub.com - NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 1772 days agogenome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vtSmudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1013 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
By BioJoker 2199 days agogithub.com - lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads...AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
By BioStar 2540 days agosourceforge.net - AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to...
