Results for "scaffolder"

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  • MeDuSa: a multi-draft based scaffolder

    MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalises the scaffolding problem by means of a co...

    Tags: MeDuSa, multi-draft, scaffolder, NGS, Genome, Assembly

    2315 days ago

  • P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

    P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and c...

    Tags: P_RNA_scaffolder, accurate, genome, scaffolder, paired-end, RNA-sequencing, reads

    2197 days ago

  • npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads

    npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple structural analyses such as gene ordering, plasmi...

    Tags: npScarf, real-time, scaffolder, SPAdes, contigs, Nanopore, sequencing, reads

    2198 days ago

  • P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

    P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides another practical alternative to existing mate-...

    Tags: P_RNA_scaffolder, fast, accurate, genome, scaffolder, paired-end, RNA, sequencing, reads, scaffold

    2110 days ago

  • gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

    gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser. gapFinisher can fill gaps in draft genom...

    Tags: gapFinisher, reliable, gap, filling, pipeline, SSPACE, LongRead, scaffolder, NGS, Tools

    1606 days ago

  • gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

    gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6733440/

    Tags: gapFinisher, reliable, gap, filling, pipeline, SSPACE-LongRead, scaffolder, output

    1495 days ago