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

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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

Just download the script.

Requirements

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].

About

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

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