Results for "pipeline"


  • #Eukaryotic #genome #annotation #scipio #pipeline

    Tags: Eukaryotic, genome, annotation, scipio, pipeline

    819 days ago

  • Webinar on Streamlining large scale analysis using the Strand NGS Pipeline Manager on 24 Feb 2016

    Live Webinar on Streamlining large scale NGS data analysis using the Strand NGS Pipeline Manager on 24 Feb 2016 Abstract: Strand NGS includes comprehensive workflows for DNA-Seq, RNA-Seq, Small RNA-Seq, ChIP-Seq, MeDIP-Seq, and Methyl-Seq analysis. Each workflow includes a quality assessment and...

    Tags: Strand NGS, data analysis, pipeline, Clinical, genomics

    751 days ago

  • Omega2: metagenome assembly pipeline

    Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming short branches. Unitigs were generated based on minimum cost flow analysis of the overlap graph and then merged to contigs and scaffolds using m...

    Tags: Omega2, metagenome, assembly, pipeline

    230 days ago

  • Unicycler: Hybrid assembly pipeline for bacterial genomes

    Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible asse...

    Tags: Unicycler, Hybrid, assembly, pipeline, bacterial, genomes

    107 days ago

  • DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication

    We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly ...

    Tags: DFAST, flexible, prokaryotic, genome, annotation, pipeline, faster, genome, publication

    103 days ago

  • Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence

    Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in ...

    Tags: Taxoblast, pipeline, identify, contamination, genomic, sequence

    94 days ago

  • ONT assembly and Illumina polishing pipeline

    This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the previous steps using BWA mem. Perform correction of contigs using p...

    Tags: ONT, assembly, Illumina, polishing, pipeline

    94 days ago

  • HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

    HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C protocols, including digestion protocols as well as protocols that do not require restriction enzyme such as DNase Hi-C. I...

    Tags: HiC-Pro, pipeline, Hi-C, processing

    81 days ago

  • 3d-dna: 3D de novo assembly (3D DNA) pipeline

    This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. Unless otherwise noted, all terminology below is consistent with t...

    Tags: 3D, de novo, assembly, 3D, DNA, pipeline

    59 days ago

  • PGAP-X: Extension on pan-genome analysis pipeline

    PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene distribution with different conservative levels, and genetic variation from pa...

    Tags: PGAP-X, Extension, pan-genome, analysis, pipeline

    33 days ago