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P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By BioStar 2268 days agowww.fishbrowser.org - P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides...AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome...
By Jit 1795 days agogithub.com - We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.Genomicus: genome browser that enables users to navigate in genomes in several dimensions
By Jit 997 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...
Structural variants PPT
By Jit 2998 days ago1000 Genomes data tutorial at ASHG Structural variants presentation by Jan Korbel European Molecular Biology Laboratory (EMBL) Heidelberg Genome Biology Research...Genobuntu: Package for Next Generation Sequencing and Genome Assembly
By BioStar 1648 days agosourceforge.net - Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.Commonly used biological software and...MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer...
By Rahul Nayak 940 days agogithub.com - MUM&Co is able to detect:Deletions, insertions, tandem duplications and tandem contractions (>=50bp & <=150kb)Inversions (>=1kb) and translocations (>=10kb)poRe: an R package for the visualization and analysis of nanopore sequencing data
By Jit 2555 days ago Comments (1)academic.oup.com - Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the...NanoPack: visualizing and processing long-read sequencing data
By Jit 2295 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 1760 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/vtFigeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 66 days agogithub.com - Tool for plotting sequencing data along genomic coordinates. FIGENO is a FIGure GENerator for GENOmics With figeno, you can plot various types of sequencing data along genomic coordinates. Video...
