Results for "Genome"

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  • swgis v2.0 : a seqword genomic island sniffer

    swgis v2.0 is the modified version of the seqword genomic island sniffer. this version is specifically optimized for predicting genomic islands in eukaryotic genomes. swgis v2.0 was tested on several eukaryotic species of different lineages. all identified genomic islands were deposited in t...

    Tags: swgis, modified, version, seqword, genomic, island, sniffer, HGT, rna, genome

    1974 days ago

  • pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks

    pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot: bigwig bed (many options) bedgraph links (represented as arcs) Hi-C matrices (if HiCExplorer is installed)

    Tags: Standalone, program, library, plot, beautiful, genome, browser, tracks

    1966 days ago

  • ASCIIGenome: genome browser based on command line interface and designed for running from console terminals.

    ASCIIGenome is a genome browser based on command line interface and designed for running from console terminals. Since ASCIIGenome does not require a graphical interface it is particularly useful for quickly visualizing genomic data on remote servers while offering flexibility sim...

    Tags: ASCIIGenome, genome, browser, command, line, interface, designed, running, console, terminals.

    1966 days ago

  • ANItools web: a web tool for fast genome comparison within multiple bacterial strains

    ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you could send us the genome sequence by email. Then ...

    Tags: ANItools, web, tool, fast, genome, comparison, multiple, bacterial, strains

    1961 days ago

  • SKESA: strategic k-mer extension for scrupulous assemblies

    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, handles low-level contamination in reads, is fast,...

    Tags: SKESA, strategic, k-mer, extension, scrupulous, assemblies, genome, assembly

    1961 days ago

  • NovoGraph: building whole genome graphs from long-read-based de novo assemblies

    NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of principle by creating a genome graph of seven ethnical...

    Tags: NovoGraph, building, whole, genome, graphs, long-read-based, de novo, assemblies

    1960 days ago

  • Merqury: reference-free quality and phasing assessment for genome assemblies

    Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of tools for this ...

    Tags: Merqury, reference-free, quality, phasing, assessment, genome, assemblies

    1391 days ago

  • Genobuntu: A software package containing more than 70 software and packages oriented towards NGS and genome assembly

    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 example script files for different assemb...

    Tags: Genobuntu, software, package, packages, oriented, NGS, assembly, genome

    1934 days ago

  • genoPlotR - plot gene and genome maps project!

    genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files. Features Linear representation of several segments of DNA Comp...

    Tags: genoPlotR, plot, gene, genome, maps, project, R

    1933 days ago

  • Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies

    Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an issue for downstream analysis whether you're wor...

    Tags: Purge, Haplotigs, Pipeline, curate, heterozygous, diploid, genome, assemblies

    1929 days ago