Results for "Assemblies"

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  • GAM-NGS: genomic assemblies merger for next generation sequencing

    GAM-NGS is a tool able to merge two or more assemblies in order to improve contiguity and correctness. It can be used on all NGS-based assembly projects and it shows its full potential with multi-library Illumina-based projects. With more than 20 available assemblers it is hard to select the best...

    Tags: GAM-NGS, Genomic, Assemblies, Merger, Sequencing, NGS

    123 days ago

  • npScarf: Scaffolding and Completing Assemblies in Real-time Fashion

    npScarf (jsa.np.npscarf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbial datasets. It also facilitates the real-time analysis of position...

    Tags: npScarf, Scaffolding, Completing, Assemblies, PacBio

    120 days ago

  • GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.

    GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which combines contig order, distance and orientation...

    Tags: GRASS, Generic, Algorithm, Scaffolding, NGS, Sequencing, Assemblies

    120 days ago

  • SuRankCo: supervised ranking of contigs in de novo assemblies

    SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet. https://bm...

    Tags: SuRankCo, Supervised, Ranking, Contigs, Assemblies

    119 days ago

  • PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies

    Genome sequencing projects sometimes uncover more organisms than expected, especially for complex and/or non-model organisms. It is therefore useful to develop software to identify mix of organisms from genome sequence assemblies. PhylOligo, a new package including tools to explore, identify and...

    Tags: PhylOligo, package, identify, contaminant, untargeted, organism, sequences, genome, assemblies

    40 days ago

  • KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies

    We present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads and de novo genome assemblies, primarily via their k-mer frequencies and GC composition. KAT enables users to assess levels of errors, bias and contaminatio...

    Tags: KAT, K-mer, analysis, toolkit, quality, control, NGS, datasets, genome, assemblies

    27 days ago