Results for "generation"

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  • Ra assembler - a de novo DNA assembler for third generation sequencing data

    Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in development since 2014 in the form of several separa...

    Tags: Ra, assembler, de novo, DNA, assembler, third, generation, sequencing, assembly

    2283 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

    2045 days ago

  • Qualimap2: Evaluating next generation sequencing alignment data

    Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. Supported types of experiments i...

    Tags: Qualimap2, Evaluating, next, generation, sequencing, alignment, coverage, plot, ngs, bam

    2026 days ago

  • nQuire: a statistical framework for ploidy estimation using next generation sequencing

    nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemente...

    Tags: nQuire, statistical, framework, ploidy, estimation, next, generation, sequencing, NGS

    2003 days ago

  • AMStat: display statistics of large sequence files from next generation sequencing projects

    SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads separately. This allows for identification of a va...

    Tags: display, statistics, large, sequence, next, generation, sequencing, projects, NGS, SAMstats

    1966 days ago

  • HASLR: a hybrid assembler which uses both second and third generation sequencing reads

    HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on all the samples compared to othe...

    Tags: HASLR, hybrid, assembler, third, generation, sequencing, reads, illumina, pacbio, ont, assembly, genome

    1425 days ago

  • McClintock: Meta-pipeline to identify transposable element insertions using next generation sequencing data

    an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods. We demonstrate the utility of McClintock by eval...

    Tags: McClintock, Meta-pipeline, identify, transposable, element, insertions, next, generation, sequencing, data

    1249 days ago

  • Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data

    Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using th...

    Tags: Platypus, Haplotype-Based, Variant, Caller, Next, Generation, Sequence, Data, NGS, SNP

    1982 days ago

  • vt: a variant tool set that discovers short variants from Next Generation Sequencing data.

    vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vt

    Tags: vt, variant, tool, discovers, short, variants, Next, Generation, Sequencing, data

    1522 days ago

  • Genobuntu: Package for Next Generation Sequencing and Genome Assembly

    Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.Commonly used biological software and example script files for different assembly p...

    Tags: Genobuntu, Package, Next, Generation, Sequencing, Genome, Assembly

    1410 days ago