Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Nextflow workflow for ONT reads QC, Assembly, Polishing and Evaluation

    Can anyone suggest if there is any comprehensive snakemake or Nextflow workflow for ONT reads QC, Assembly, Polishing and Evaluation?

  • #2
    nf-core's nanoseq workflow is not a bad place to start ? https://nf-co.re/nanoseq

    Comment


    • #3
      ​Yes, there are several existing snakemake and Nextflow workflows for ONT read QC, assembly, polishing, and evaluation. Here are a few examples:squidward
      ONT-pipeline: This is a Nextflow pipeline for ONT read QC, assembly, polishing, and evaluation. It includes modules for read QC using NanoPlot, assembly using Flye or Canu, polishing using Racon or Medaka, and evaluation using QUAST or BUSCO. The pipeline is highly configurable and can be customized to fit different sequencing and analysis needs.
      SnakeMake-ONT: This is a snakemake-based pipeline for ONT read QC, assembly, polishing, and evaluation. It includes modules for read QC using NanoPlot, assembly using Flye, polishing using Racon, and evaluation using QUAST. The pipeline is designed to be highly modular and extensible, allowing users to easily add or remove analysis steps as needed.
      ONTQC: This is a snakemake-based pipeline for ONT read QC and filtering. It includes modules for read QC using NanoPlot, read filtering using Filtlong or qcat, and read correction using Canu or Racon. The pipeline is optimized for long-read sequencing data and can handle large datasets with ease.
      These workflows are just a few examples of the many available options for ONT read QC, assembly, polishing, and evaluation. It is important to carefully evaluate each workflow to determine which one best fits your specific needs and requirements.

      Comment


      • #4
        Pipeline used for de novo genome assembly @CNAG. Contribute to cnag-aat/assembly_pipeline development by creating an account on GitHub.


        This is our pipeline that we're using internally. Installation outside our cluster is not extensively tested, but it shouldn't be that hard to get up and running. Everything necessary is installed via conda except for two optional tools: NextDenovo and NextPolish, which need to be installed separately and available in your PATH.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Essential Discoveries and Tools in Epitranscriptomics
          by seqadmin


          The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...
          Yesterday, 07:01 AM
        • seqadmin
          Current Approaches to Protein Sequencing
          by seqadmin


          Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
          04-04-2024, 04:25 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 04-11-2024, 12:08 PM
        0 responses
        43 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 10:19 PM
        0 responses
        43 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 09:21 AM
        0 responses
        38 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-04-2024, 09:00 AM
        0 responses
        55 views
        0 likes
        Last Post seqadmin  
        Working...
        X