Results for "Analysis"

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  • Fancy Oneliner for Bioinformatics !!

    This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You can copy/paste the commands as they are in your terminal screen, provided you follow the same naming conventions and folder struct...

    Tags: Bioinformatics, Analysis, Visualization, SAM, BAM, Oneliner, NGS, metagenomics

    259 days ago

  • Scarpa

    Scarpa is a stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate insert size distributions from data. Scarpa is ...

    Tags: Bioinformatics, Analysis, NGS, Scaffolding, Scarpa

    253 days ago

  • WiseScaffolder

    Function WiseScaffolder is a stand-alone semi-automatic application for genome scaffolding of pre-assembled contigs using mate-pair data. It also produces editable scaffold maps, allowing either to build gapped scaffolds or usable as a common thread for the manual improvement of scaffolds. Desc...

    Tags: Bioinformatics, Analysis, NGS, Scaffolding, WiseScaffolder

    253 days ago

  • MEGAN6

    Microbiome analysis using a single application MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application. Taxonomic analysis using the NCBI taxonomy or a customized taxonomy such as SILVA Functional analysis using Int...

    Tags: Bioinformatics, Analysis, NGS, Taxonomy, Functional Analysis

    241 days ago

  • Genome STRiP

    Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals.Genome STRiP looks both across and within a set of sequenced...

    Tags: Bioinformatics, Analysis, NGS, Genome STRiP, Genome, Variation

    198 days ago

  • VAGUE:Velvet Assembler Graphical Front End

    VAGUE is a vague acronym for "Velvet Assembler Graphical Front End", which means it is a GUI for the Velvet de novo assembler. The command line version of Velvet can be complicated for beginners to use, but VAGUE makes it clear and simple More at http://www.vicbioinformatics.com/software.va...

    Tags: Bioinformatics, Analysis, Assembly, Genome, VAGUE, Plot, View, Valvet

    27 days ago

  • CrossMap

    CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file...

    Tags: Bioinformatics, Analysis, NGS, CrossMap, Genome, Coordinates

    199 days ago

  • valet

    VALET is a pipeline for performing de novo validation of metagenomic assemblies. VALET checks a number of properties that should hold true for a correct assembly (e.g., mate-pairs are aligned at the correct distance from each other in the assembly, the depth of coverage is fairly un...

    Tags: Bioinformatics, Analysis, NGS, Valet, Genome

    182 days ago

  • OrganellarGenomeDRAW

    OrganellarGenomeDRAW is dedicated to convert genetic information stored in GenBank entries to graphical maps. The input text file has to be in GenBank flat file format, whereas the output format can be chosen among several formats. The application is especially optimized and adapted for the ...

    Tags: Bioinformatics, Analysis, NGS, OrganellarGenomeDRAW, Draw, Genome, OGDRAW

    219 days ago

  • RepeatModeler

    RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from se...

    Tags: Bioinformatics, Analysis, NGS, Repeats, TE, RepeatModeler, RECON, de-novo, family, Genome

    217 days ago