nanoQC: A Nextflow repository from ayoraind

Pre-assembly QC workflow for ONT.

Usage


=======================================================================
  PRE-ASSEMBLY QC: TAPIR Pipeline version 1.0dev
=======================================================================
 The typical command for running the pipeline is as follows:
        nextflow run main.nf --reads "PathToReadFile(s)" --output_dir "PathToOutputDir"  

        Mandatory arguments:
         --reads                        Query fastq.gz file of sequences you wish to supply as input (e.g., "/MIGE/01_DATA/01_FASTQ/T055-8-*.fastq.gz")
         --output_dir                   Output directory to place output (e.g., "/MIGE/01_DATA/03_ASSEMBLY")
         
        Optional arguments:
         --help                         This usage statement.
         --version                      Version statement

Introduction

This pipeline generates pre-assembly QC plots of a Long Read Dataset. To learn more about nanoQC, check out the original author's github page.

Sample command

An example of a command to run this pipeline is:

nextflow run main.nf --reads "Sample_files/*.fastq.gz" --output_dir "test2"

Word of Note

This is an ongoing project at the Microbial Genome Analysis Group, Institute for Infection Prevention and Hospital Epidemiology, Üniversitätsklinikum, Freiburg. The project is funded by BMBF, Germany, and is led by Dr. Sandra Reuter.

Authors and acknowledgment