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.
-
nf-core's nanoseq workflow is not a bad place to start ? https://nf-co.re/nanoseqLeave 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?
-
Developments in sequencing technologies and methodologies have transformed the field of epigenetics, giving researchers a better way to understand the complex world of gene regulation and heritable modifications. This article explores some of the diverse sequencing methods employed in the study of epigenetics, ranging from classic techniques to cutting-edge innovations while providing a brief overview of their processes, applications, and advances.
Methylation Detect...05-31-2023, 10:46 AM -
Differential Expression and Data Visualization: Recommended Tools for Next-Level Sequencing Analysis
After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we’re wrapping up with a discussion about tools for differential gene expression analysis and data visualization. In this article, we include recommendations from the following experts: Dr. Mark Ziemann, Senior Lecturer in Biotechnology and Bioinformatics, Deakin University; Dr. Medhat Mahmoud Postdoctoral Research Fellow at Baylor College of Medicine;...05-23-2023, 12:26 PM -
Continuing from our previous article, we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat Mahmoud, Postdoctoral Research Fellow at Baylor College of Medicine, and Dr. Ming "Tommy" Tang, Director of Computational Biology at Immunitas and author of From Cell Line to Command Line.
Variant detection and analysis tools
Mahmoud classifies variant detection work into two main groups: short variants (<50...05-19-2023, 10:03 AM
Leave a comment: