Information about Fastq QC Report

Table of Contents

Overview

Raw data processing pipeline also generate basic quality reports for the fastq files using the following tools:

  • FastQC for fastq reads quality check. See the official FastQC help documents for more detail.
  • FastQ Screen for sample (species) contamination check
  • MultiQC for merging all the reports (for all samples) together and for creating a top-level summary report of each lane (per project)
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List of genomes included for FastQ Screen analysis

  • Human (HG38)
  • Mouse (mm10)
  • Ecoli (Escherichia_coli_K_12_MG1655)
  • PhiX
  • Staphylococcus
  • Adapters (FastQC contaminats file)
  • Mycobacterium (Mycobacterium_tuberculosis_H37RV)
  • Vectors (UniVec)
  • Mycoplasma (GCF_000027345.1_ASM2734v1)
  • Rhodococcus
  • Paenibacillus
  • Human coronavirus 229E (NC_002645.1)
  • Human coronavirus OC43 (AY391777.1)
  • Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1 (NC_045512.2)
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Software and version information

FastQC command line

Example FastQC command.


  fastqc 
    -q
    --noextract
    -f fastq 
    -k 7 
    -t 1
    -o /path/fastqc_output
    -d /path/temp_work_dir 
    /path/fastq_file
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FastQ Screen command line

Example FastQ Screen command.


  fastqscreen
    --conf fastqscreen_conf
    --outdir /path/fastqscreen_output
    --aligner bowtie2
    --force
    --quiet
    --subset 100000
    --threads 1
    /path/fastq_file
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List of resources

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Change logs

  • 20 December 2020
    • Updated MultiQC from v 1.7 to v 1.9
  • 25th March 2020
    • Added Human coronavirus references to fastq_screen
  • 24th April 2019
    • Updated MultiQC from v 1.6 to v 1.7
  • 2018 July 01
    • Updated MultiQC from v1.2