Results for "de novo"

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  • Want to Know which genome assembler rule the world ?

    Assemblathon 2: evaluating de novo methods of genome assembly  http://www.gigasciencejournal.com/content/2/1/10/abstract http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searching.html http://assemblathon.org/post/44431915644/feedback-and-analysis-of-the-assemblat...

    Tags: Sequencing, DNA, Genome Assembly, Assembler, Omics, de novo

    1588 days ago

  • Platanus

    Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data. The latest version is 1.2.4. To cite Platanus, please use the following: Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y,...

    Tags: Bioinformatics, NGS, Assembly, de novo, Sequence, Assembler, Heterozygous

    583 days ago

  • miniasm: very fast OLC-based de novo assembler for noisy long reads

    Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. I...

    Tags: Ultrafast, de novo, assembly, long, noisy, reads, consensus

    19 days ago

  • Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome

    Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make...

    Tags: Oxford, Nanopore, Sequencing, Hybrid, Error, Correction, de novo, Assembly, Eukaryotic, Genome

    17 days ago

  • 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

    12 days ago

  • Meraculous: De Novo Genome Assembly with Short Paired-End Reads

    We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, wi...

    Tags: Meraculous, De Novo, Genome, Assembly, Short, Paired-End, Reads

    40 days ago