Results for "Tool"

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  • DAVI: Deep learning-based tool for alignment and single nucleotide variant identification

    DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools used for bench-marking. We further demonstrate tha...

    Tags: DAVI, deep, alignment, variant, identification, tool, snp

    1108 days ago

  • FQC Dashboard: Integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool

    FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The dashboard groups samples in dropdowns for navigat...

    Tags: FQC, Dashboard, Integrates, FastQC, results, web-based, interactive, extensible, FASTQ, quality, tool

    1234 days ago

  • EXCAVATOR2tool

    EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing (WES) data to identify CNVs. EXCAVATOR2 enhances the identification of all genomic CNVs, both overlapping and non-overlapping targeted exons by integrating the analysis of In-targets and Off- ...

    Tags: Bioinformatics, Analysis, CNV, EXCAVATOR2, tool, NGS

    2675 days ago

  • TelomereHunter

    TelomereHunter is a tool for estimating telomere content from human whole-genome sequencing data. It is designed to take BAM files from a tumor and a matching control sample as input. However, it is also possible to run TelomereHunter with one input file. TelomereHunter extracts and sorts telomer...

    Tags: TelomereHunter, tool, telomere, human, whole-genome, sequencing

    2246 days ago

  • Circleator

    The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of genome-associated data, like this one: Common uses of the to...

    Tags: Circleator, Perl, visualization, tool

    2468 days ago

  • Perlbrew: admin-free perl installation management tool.

    perlbrew is an admin-free perl installation management tool. The latest version is 0.79, read the release note: Release 0.79.  Copy & Paste this line into your terminal: \curl -L https://install.perlbrew.pl | bash Or, if your system does not have curl but something else: # Lin...

    Tags: admin-free, perl, installation, management, tool

    2451 days ago

  • Mulan: MUltiple sequence Local AligNment and conservation visualization tool

    Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It combines refine and tba tool...

    Tags: Mulan, MUltiple, sequence, Local, AligNment, conservation, visualization, tool

    2443 days ago

  • RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities

    RAMI, which clusters related nodes in a phylogenetic tree based on the patristic distance. RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly. Availability: RAMI is licensed under GNU GPL and can be run or downloaded from&n...

    Tags: RAMI, tool, identification, characterization, phylogenetic, clusters, microbial, communities

    2425 days ago

  • CHSMiner: a GUI tool to identify chromosomal homologous segments

    Background The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degeneration of CHSs. Results Here we present a Java software CHSMiner tha...

    Tags: CHSMiner, GUI, tool, identify, chromosomal, homologous, segments

    2322 days ago

  • PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool

    PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture, PLAST takes full advantage of recent multi-core...

    Tags: PLAST, fast, accurate, NGS, scalable, bank-to-bank, sequence, similarity, search, tool

    2309 days ago