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

[chayan]

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

[foreveremain]

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

[helendam]

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.

[talioto]

https://github.com/cnag-aat/assembly_pipeline

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.