Results for "analysis"


  • OPERA : Optimal Paired-End Read Assembler

    OPERA (Optimal Paired-End Read Assembler) is a sequence assembly program ( It uses information from paired-end/mate-pair/long reads to order and orient the intermediate contigs/scaffolds assembled in a genome assembly project, in a process known as ...

    Tags: Bioinformatics, Analysis, NGS, OPERA, Assembler, Genome

    501 days ago


    Fermi is a de novo assembler with a particular focus on assembling Illumina short sequence reads from a mammal-sized genome. In addition to the role of a typical assembler, fermi also aims to preserve heterozygotes which are often collapsed by other assemblers. Its ultimate goal is...

    Tags: Bioinformatics, Analysis, NGS, FERMI, Assembler, Genome

    501 days ago

  • VirMet

    Watch out: only a few files are counted in coverage statistics. Full documentation on Read the Docs. A set of tools for viral metagenomics. virmet is called with a command subcommand syntax: virmet fetch --viral n, for example, downloads the bacterial database. Other available subcom...

    Tags: Bioinformatics, Analysis, NGS, VirMet, Genome, MetaGenome

    470 days ago


    Metagenomics sequencing projects collect samples of DNA from uncharacterized environments that may contain hundreds or even thousands of species. One of the main challenges in analyzing a metagenome is phylogenetic classification of raw sequence reads into groups representing the same or similar ...

    Tags: Bioinformatics, Analysis, NGS, PHYMMBL, Genome, MetaGenome, Classification, Reads

    470 days ago

  • Ribbon !!

    Visualization has played an extremely important role in the current genomic revolution to inspect and understand variants, expression patterns, evolutionary changes, and a number of other relationships. However, most of the information in read-to-reference or genome-genome alignments is lost for ...

    Tags: Bioinformatics, Analysis, NGS, Visualization, Genome, Rearrangement, Ribbon

    459 days ago

  • Shinyheatmap

    Background: Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well a...

    Tags: Bioinformatics, Analysis, NGS, HeatMap, Genome, Shinyheatmap, R, Visualize, Map, Transcriptomics, Metabolomics, Metagenomics

    459 days ago

  • GenomeScope: open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate, and repeat content from unprocessed short reads

    Summary: GenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate, and repeat content from unprocessed short reads. These features are essential for studying genome evolution, and help to choose para...

    Tags: Bioinformatics, Analysis, NGS, GenomeScope, Genome, Stats, Estimate, Heterozygosity, repeat content, Statistical

    51 days ago

  • Graph Genome Suite

    Seven Bridges is the biomedical data analysis company accelerating breakthroughs in genomics research for cancer, drug development and precision medicine. We build self-improving systems to analyze millions of genomes, including the Graph Genome Suite — the most advanced populatio...

    Tags: Bioinformatics, Analysis, NGS, Network, Graph

    452 days ago

  • eFORGE.v1.2

    The eFORGE tool provides a method to view the tissue specific regulatory component of a set of EWAS DMPs. eFORGE analysis takes a set of DMPs, such as those hits above genome-wide significance threshold in an EWAS study, and analyses whether there is enrichment for overlap of putative functional ...

    Tags: Bioinformatics, Analysis, NGS, eFORGE, Genome, EWAS

    452 days ago

  • HybPiper

    HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughpu...

    Tags: Bioinformatics, Analysis, NGS, HybPiper, Genome, Network, Capture, Genes

    445 days ago