layout | title |
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fastq_qc_template |
IGF help pages - Fastq QC |
- Overview
- List of genomes included for FastQ Screen analysis
- Software and version information
- List of resources
- Change logs
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)
- 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)
Example FastQC command.
fastqc -q --noextract -f fastq -k 7 -t 1 -o /path/fastqc_output -d /path/temp_work_dir /path/fastq_file
Example FastQ Screen command.
fastqscreen --conf fastqscreen_conf --outdir /path/fastqscreen_output --aligner bowtie2 --force --quiet --subset 100000 --threads 1 /path/fastq_file
- FastQC
- FastQC help
- Example of a good quality Illumina data (FastQC)
- Example of a bad quality Illumina data (FastQC)
- FastQ screen
- MultiQC
- 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