Results for "Scaffolding"


  • 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

    592 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

    592 days ago

  • pyScaf

    pyScaf orders contigs from genome assemblies utilising several types of information: paired-end (PE) and/or mate-pair libraries (NGS-based mode) long reads (NGS-based mode) synteny to the genome of some related species (reference-based mode) Scaffolding  In reference-based mode, pyS...

    Tags: Bioinformatics, Chromosome, Genome, NGS, Align, Compare, Similarity, Scaffolding

    433 days ago


    SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or matepair data, SSPACE is able to assess the order...

    Tags: Bioinformatics, SSPACE, Scaffolding, NGS, Genome, Contig

    296 days ago

  • CLA: Contig-Layout-Authenticator

    To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CL...

    Tags: Bioinformatics, Analysis, Scaffolding, CLA, Contig

    296 days ago

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

    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

    278 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

    278 days ago

  • Opera: An optimal genome scaffolding program

    Opera (Optimal Paired-End Read Assembler) is a sequence assembly program ( ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads.An updated version called OPERA-LG has b...

    Tags: Opera, optimal, genome, scaffolding, program

    90 days ago