Results for "read"

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  • PureCN: copy number calling and SNV classification using targeted short read sequencing

    This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number...

    Tags: PureCN, copy, number, calling, SNV, classification, targeted, short, read, sequencing

    2090 days ago

  • SimLoRD: A read simulator for third generation sequencing reads

    SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference can be read from a FASTA file or randomly gener...

    Tags: SimLoRD, read, simulator, third, generation, sequencing, reads, Pacific, Biosciences, SMRT, error, model

    2076 days ago

  • rHAT: a seed-and-extension-based noisy long read alignment tool

    rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT) sequencing reads.

    Tags: rHAT, seed-and-extension-based, noisy, long, read, alignment, tool, ont, pacbio

    2045 days ago

  • BamView: a free interactive display of read alignments in BAM data files

    To run the application on UNIX from the downloaded jar file run the UNIX: java -mx512m -jar BamView.jar and extra command line options are given when '-h' is used: java -jar BamView.jar -h BAM files can be specified on the command line with the '-a' option: java -mx512m -jar BamView.jar -a p...

    Tags: BamView, free, interactive, display, read, alignments, BAM, data, files

    1997 days ago

  • ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment

    ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment, viz., the recoverability of the TF binding motif, accuracy of TF-DNA binding detection, the sensitivity of inferred TF-DNA bindin...

    Tags: ChIPulate, Python3, framework, simulate, read, counts, ChIP-seq, experiment

    1861 days ago

  • Shasta long read assembler

    The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. Computational methods used by the Shasta assembler include: Using a run-length representation of the read sequence...

    Tags: Shasta, long, read, genome, assembler, tools, ngs

    1567 days ago

  • URMAP, an ultra-fast read mapper

    URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves high accuracy (precision 0.998, sensitivity 0.982...

    Tags: URMAP, ultra-fast, read, mapper

    1277 days ago

  • Metabuli 분리 improves metagenomic read classification

    Metabuli 분리 improves metagenomic read classification through metamers, DNA-AA k-mers, to be sensitive and specific, recovering 99% and 98% of DNA or AA classifiers.   Metabuli is metagenomic classifier that jointly analyze both DNA and amino acid (AA) sequences. DNA-based classifiers can m...

    Tags: Metabuli, 분리, metagenomic, read, classification, metamers, DNA-AA, k-mers, sensitive, and specific, DNA, AA, classifiers

    330 days ago