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ARCS: scaffolding genome drafts with linked reads
By Rahul Nayak 2483 days agogithub.com - ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiensgenome assembly can be increased over...Genomicus: genome browser that enables users to navigate in genomes in several dimensions
By Jit 1028 days agowww.genomicus.bio.ens.psl.eu - Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. Once a query gene has been entered, it...Jvarkit : Java utilities for Bioinformatics
By Jit 2390 days agolindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for Bioinformatics
Frequent Paired-end reads (PE 2x100) mapping command lines
Last updated 2414 days ago by Jitbowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ && bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq > r12.bwa.sam bwa bwasw...Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
By Rahul Nayak 2257 days agosourceforge.net - Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like...Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 2552 days agogithub.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in...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 2193 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 MG1655
