Our Sponsors
Related items
Libraries or management tools for high throughput sequencing data
Last updated 80 days ago by LEGEGATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.These methods enable the analysis of data sets of any size on multi-core desktop...
String graph based genome assembly software and tools !
By Rahul Nayak 2561 days agoIn graph theory, a string graph is an intersection graph of curves in the plane; each curve is called a "string". String graphs were first proposed by E. W. Myers in a 2005 publication.Genome assembly stats plotting
By Jit 2490 days agogithub.com - A de novo genome assembly can be summarised b y a number of metrics, including: Overall assembly length Number of scaffolds/contigs Length of longest scaffold/contig Scaffold/contig N50 and N90Assembly base composition, in...SWALO: Scaffolding with assembly likelihood optimization
By Jit 2378 days agoatifrahman.github.io - SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to...Converting a VCF into a FASTA given some reference !
By Jit 2348 days agoconverting a VCF file into a FASTA file given a reference sequenceSKESA: strategic k-mer extension for scrupulous assemblies
By Jit 2231 days agogithub.com - SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity,...Versatile genome assembly evaluation with QUAST-LG
By Jit 2194 days agocab.spbu.ru - QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size). QUAST-LG is included in the QUAST package starting from version 5.0.0 (download the latest release). Run QUAST as...List of tools frequently used while genome assembly
By BioStar 2162 days agoTo decide which strategy should be our “preferred” genome assembly approach based on data rather than my gut-feeling about the “best assembly” I decided to do some testing with a known “true” reference E Coli K12 MG1655TRITEX sequence assembly pipeline for Triticeae genomes
By Jit 1952 days agotritexassembly.bitbucket.io - The pipeline is open-source and hosted in a public Bitbucket repository. TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable...JCVI:Python utility libraries on genome assembly, annotation and comparative genomics
By Jit 1742 days agogithub.com - Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. https://github.com/tanghaibao/jcvi More at https://github.com/tanghaibao/jcvi/wiki
