Results for "whole"

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  • karyoploteR: plot whole genomes with arbitrary data

    karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR is to offer the user an easy way to plot data a...

    Tags: karyoploteR, plot, whole, genomes, NGS, arbitrary, data, karyotype

    1945 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

    2334 days ago

  • Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

    Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up ...

    Tags: Magic-BLAST, mapping, next-generation, RNA, DNA, sequencing, whole, genome, transcriptome.

    2316 days ago

  • AliTV—interactive visualization of whole genome comparisons

    AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based an...

    Tags: AliTV, interactive, visualization, whole, genome, comparisons

    2301 days ago

  • ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data

    ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with the help of a Bloom filter that represents the k...

    Tags: ChopStitch, exon, annotation, splice, graph, transcriptome, assembly, whole, genome, sequencing

    2127 days ago

  • Genome U-Plot: a whole genome visualization

    Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution an...

    Tags: Genome, U-Plot, whole, genome, visualization

    2117 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

    1992 days ago

  • shinyChromosome:a GUI for the interactive creation of non-circular whole genome diagrams

    shinyChromosome is a graphical user interface for interactive creation of non-circular whole genome diagrams developed using the R Shiny package. To create single-genome plot by aligning genome data along all chromosomes of a single genome, go to the Single-genome plot menu. To cretae two-genom...

    Tags: shinyChromosome, GUI, interactive, creation, non-circular, whole, genome, diagrams

    1521 days ago

  • Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data

    This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analy...

    Tags: Smudgeplot, Inference, ploidy, heterozygosity, structure, whole, genome, sequencing, data

    794 days ago

  • Darwin-WGA: A Co-processor Provides Increased Sensitivity in Whole Genome Alignments with High Speedup

    Darwin-WGA, is the first hardware accelerator for whole genome alignment and accelerates the gapped filtering stage. Darwin-WGA also employs GACT-X, a novel algorithm used in the extension stage to align arbitrarily long genome sequences using a small on-chip memory, that provides better quality ...

    Tags: Darwin-WGA, Co-processor, Increased, Sensitivity, Whole, Genome, Alignments, High, Speedup

    1843 days ago