Results for "genome"

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  • Bandage: interactive visualization of de novo genome assemblies

    Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colors and extracting sequ...

    Tags: Bandage, interactive, visualization, de novo, genome, assemblies

    82 days ago

  • COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

    An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, whic...

    Tags: COPE, accurate, k-mer, pair-end, reads, connection, tool, genome, assembly

    81 days ago

  • Why are de Bruijn #graphs useful for #genome #assembly? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5531759/

    Tags: graphs, genome, assembly

    79 days ago

  • jobTree based python wrapper to run the genome simulation tool suite Evolver

    evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation as it runs including text and image files. Also...

    Tags: jobTree, python, wrapper, genome, simulation, tool, suite, Evolver

    78 days ago

  • kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome

    Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages 9-10) in the version 3.1 User Guide. Thanks to To...

    Tags: kSNP3.0, SNP, detection, phylogenetic, analysis, genomes, alignment, reference, genome

    78 days ago

  • Mugsy: multiple whole genome alignment tool

    Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FA...

    Tags: Mugsy, multiple, whole, genome, alignment, tool

    78 days ago

  • Tools for bacterial whole genome annotation

    RAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annotation and pathway analysis. Takes several hours per genome but I think this is the best way to get a high quality annotation (if you have only a few genomes to annotate). Pr...

    Tags: Tools, bacterial, whole, genome, annotation, prokaryotic, genes

    70 days ago

  • Mash: fast genome and metagenome distance estimation using MinHash

    Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is available in and GCC >= 4.8 and OSX >= 10....

    Tags: Mash, fast, genome, metagenome, distance, estimation, MinHash

    74 days ago

  • String graph based genome assembly software and tools !

    In graph theory, a string graph is an intersection graph of curves in the plane; each curve is called a "string".  String graphs were first proposed by E. W. Myers in a 2005 publication. In recent Genome Research paper describing an...

    Tags: String, graph, genome, assembly, software, tools !

    67 days ago

  • Delta: a new Web-based 3D genome visualization and analysis platform

    Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the 3D physical architecture of genomes. Delta takes Hi-C or ChIA-PET contact matrix as input and predicts the topologically associating domains and chromatin loops in the ge...

    Tags: Delta, Web-based, 3D, genome, visualization, analysis, platform

    66 days ago