Rahul Nayak
A Bioinformatician
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ECTOOLS: Long Read Correction and other Correction tools
By Jit 3074 days agogithub.com - Long Read Correction and other Correction tools This package is a loose collection of scripts. To run the correctionroutine see the section below. Descriptions of the other scriptsare at the bottom of this file. Contact: gurtowsk@cshl.edu In...
Gap filling or Contigs extensions tools !
Last updated 2927 days ago by Rahul NayakThere are many tools to perform gap filling using Illumina short reads, for example "GapFiller: a de novo assembly approach to fill the gap within paired reads" or "Toward almost closed genomes with GapFiller". There are also some tools like...molinspiration: broad range of cheminformatics software tools supporting molecule manipulation
By BioJoker 2694 days agowww.molinspiration.com - Molinspiration offers broad range of cheminformatics software tools supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation,...wgd—simple command line tools for the analysis of ancient whole-genome duplications
By LEGE 2144 days agogithub.com - wgd is a easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and colinearity analysis workflows together with tools for modeling and visualization, rendering these...Frequently used bioinformatics tools for viral genome analysis !
By Neel 1809 days agoFrequently used bioinformatics tools for viral genome analysis !Bioinformatic tools for pathogens informatics at CVR
By Abhi 727 days agohttps://bioinformatics.cvr.ac.uk/software/GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
By Abhimanyu Singh 3301 days agogithub.com - GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which...Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 2166 days agogithub.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 3113 days agogithub.com - Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2787 days agogithub.com - new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE...
