Neel
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MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 2366 days agogithub.com - MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and...P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By BioStar 2247 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 1775 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 976 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...Hagfish - assess an assembly through creative use of coverage plots
By Abhi 3087 days agogithub.com - Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or...Genobuntu: Package for Next Generation Sequencing and Genome Assembly
By BioStar 1628 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 919 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 2535 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 2275 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 1739 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/vt
