nanoQC

This script is designed to automate the quality control (QC) analysis of Nanopore sequencing data files. It reads a table of barcodes and sample names, concatenates *.fastq.gz files, renames them according to sample names, and generates a comprehensive QC summary report using NanoPlot.

Table of Contents

• Installation
• Requirements
• Input table format
• Usage
• Output
• Contact

Installation

Just download the script.

Requirements

• Porechop
• NanoPlot

Ensure this tools are installed and accessible in your PATH. Be kind and please acknowledge these great authors too!

Input table format

The input table must have two columns:

• The first column contains the names of the barcodes you wish to analyze.
• The second column contains the sample names corresponding to those barcodes. Example:

  barcode-1 sample_name-1
  barcode-2 sample_name-2
  barcode-3 sample_name-3
  ...
  barcode-n sample_name-n
  

Usage

Execute the script at the fastq_pass directory or where the barcode directories are. To run the script, use the following command:

./nanoQC.sh -t <TABLE> -g <GENOME_SIZE> -o <OUTPUT_BASENAME>

Options

• -t Table file OR path to the table file containing barcodes and sample names.
• -g Genome size for depth calculation. An integer > 0.
• -o Output file basename.
• -h Display usage information.

Example

./nanoQC.sh -t E_coli_barcodes.tsv -g 5000000 -o E_coli

Output

• A fastq.gz file and a *_trimmed.fastq.gz file named according to the sample name and barcode number.
• A summary table for all the samples named output_basename_nanoplot_summary.tsv containing the following columns: sample_name, number_of_reads, number_of_bases, median_read_length, mean_read_length, read_length_stdv, n50, mean_qual, median_qual, and mean_depth.
• A nanoplot directory containing the full Nanoplot report for each sample.

Contact

For questions or issues, please open an issue in this repository or contact [email protected].