Results for "Alignments"

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  • Alignment of closely related whole genomes/scaffolds

    With the relative ease and low cost of current generation sequencing technologies has led to a dramatic increase in the number of sequenced genomes for species across the tree of life. This increasing volume of data requires tools that can quickly compare multiple whole-genome sequences, millions...

    Tags: Whole genome, NGS, Genome, Scaffolds, pan-genome, Evolution, Alignments, Compare

    2981 days ago

  • Kraken: ultrafast metagenomic sequence classification using exact alignments

    Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify sm...

    Tags: Bioinformatics, Kraken, Metagenomic, Sequence, Classification, Alignments, NGS

    2831 days ago

  • Kaiju

    Kaiju is a program for the taxonomic classification of metagenomic high-throughput sequencing reads. Each read is directly assigned to a taxon within the NCBI taxonomy by comparing it to a reference database containing microbial and viral protein sequences. By default, Kaiju uses either the avai...

    Tags: Bioinformatics, Kaiju, Metagenomic, Sequence, Classification, Alignments, NGS

    2831 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

    1811 days ago

  • CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R

    CRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 2019). It reimplements the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast and covers all necessary steps from sequence similarity searches, codon alignments to Ka/Ks calculations and synteny. The new R package tar...

    Tags: CRBHits, Conditional, Reciprocal, Best, Hits, Codon, Alignments, Ka/Ks, R

    1233 days ago

  • Ribbon: Visualizing complex genome alignments and structural variation:

    Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right. Local installation: You can install Ribbon locally from Github by following the instructions ...

    Tags: Ribbon, Visualizing, complex, genome, alignments, structural variation

    2311 days ago

  • Many-to-many pairwise alignments of two sequence sets

    needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two sequences along their entire length. The algori...

    Tags: Many-to-many, pairwise, alignments, sequence, sets, needleall, Needleman-Wunsch

    2109 days ago

  • pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file

    pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quiver if --forQuiver optio...

    Tags: pbalign, maps, PacBio, reads, reference, sequences, alignments, BAM, NGS

    2135 days ago

  • GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments

    GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap closure. We demonstrate with sequencing data from...

    Tags: GMcloser, close, gaps, assemblies, accurately, likelihood-based, selection, contig, long-read, alignments, Genome, Assembly

    2117 days ago

  • STELLAR: fast and exact local alignments

    STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar. 

    Tags: STELLAR, fast, exact, local, alignments

    2038 days ago