Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • talioto
    replied
    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.

    Leave a comment:


  • helendam
    replied
    ​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.

    Leave a comment:


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

    Leave a comment:


  • 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?

Latest Articles

Collapse

  • 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
  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM

ad_right_rmr

Collapse

News

Collapse

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