Results for "genome"

Tags

  • Scribl : HTML5 canvas genomics graphic library

    Scribl is a javascript, Canvas-based graphics library that easily generates biological visuals of genomic regions, alignments, and assembly data. Scribl can also be used in conventional offline pipelines, since everything needed to generate charts can be contained in a single html file.  

    Tags: Scribl, HTML5, canvas, genomics, graphic, library, view, genome

    1982 days ago

  • QUAST-LG: Versatile genome assembly evaluation

    QUAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a concept of upper bound assembly for ...

    Tags: QUAST-LG, Versatile, genome, assembly, evaluation

    1982 days ago

  • MITOS: improved de novo metazoan mitochondrial genome annotation

    Allows automatic annotation of metazoan mitochondrial genomes. MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. The software allows for a systematic error screening, the standardisation of gene name and gene boundary designation, anticodon labe...

    Tags: MITOS, improved, de novo, metazoan, mitochondrial, genome, annotation

    1981 days ago

  • Synima: a Synteny imaging tool for annotated genome assemblies

    Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for the...

    Tags: Synima, Synteny, imaging, tool, annotated, genome, assemblies

    1977 days ago

  • 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

    1975 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

    1967 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.

    1967 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

    1962 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

    1962 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

    1961 days ago