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, perform trimming using porechop, generates a comprehensive QC summary report using NanoPlot and a taxonomic report using Kraken2.

Table of Contents

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

Installation

Just download the script and make it executable.

chmod +x nanoQC.sh

Requirements

• porechop
• NanoPlot
• Kraken2

Ensure this tools are installed and accessible in your PATH. Be kind and please acknowledge these great devs 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> -k <KRAKEN_DB> -g <GENOME_SIZE> -o <OUTPUT_BASENAME>

Options

• -t Table file OR path to the table file containing barcodes and sample names.
• -k Directory OR path to the directory of the Kraken2 database
• -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 -k /path/to/kraken_db/directory -g 5000000 -o E_coli

Output

All the outputs will be at the output_basename_analysis directory:

• A fastq_raw directory where the *.fastq.gz files are.
• A fastq_trimmed directory where the *_trimmed.fastq.gz files are. Inside this directory you will also find a summary table for all the samples named output_basename_nanoplot_summary.tsv and two subdirectories: nanoplot and kraken2.
  • nanoplot directory contains the Nanoplot report for each sample.
  • kraken2 directory contains the kraken2 report for each sample.

Contact

For questions or issues, please open an issue in this repository or contact facundogcuba@gmail.com.