Basic Sequence QC

A generic pipeline that can be run on an arbitrary set of Illumina sequence files, regardless of the project or organism of interest.

Sequence quality information

Analyses

fastp: Collect sequence QC stats

Usage

nextflow run BCCDC-PHL/basic-sequence-qc \
  [--prefix 'prefix'] \
  --fastq_input <your fastq input directory> \
  --outdir <output directory>

Alternatively, a sample_sheet.csv file can be provided, with fields:

ID
R1
R2

For example:

ID,R1,R2
SAMPLE-01,/path/to/SAMPLE-01_R1.fastq.gz,/path/to/SAMPLE-01_R2.fastq.gz
SAMPLE-02,/path/to/SAMPLE-02_R1.fastq.gz,/path/to/SAMPLE-02_R2.fastq.gz
SAMPLE-03,/path/to/SAMPLE-03_R1.fastq.gz,/path/to/SAMPLE-03_R2.fastq.gz

The sample_sheet.csv file can be provided using the --sample_sheet_input flag as follows:

nextflow run BCCDC-PHL/basic-sequence-qc \
  [--prefix 'prefix'] \
  --sample_sheet_input <your sample_sheet.csv file> \
  --outdir <output directory>

Output

A single output file in .csv format will be created in the directory specified by --outdir. The filename will be basic_qc_stats.csv. If a prefix is provided using the --prefix flag, it will be prepended to the output filename, for example: prefix_basic_qc_stats.csv.

The output file includes the following headers:

sample_id
total_reads_before_filtering
total_reads_after_filtering
total_bases_before_filtering
total_bases_after_filtering
read1_mean_length_before_filtering
read1_mean_length_after_filtering
read2_mean_length_before_filtering
read2_mean_length_after_filtering
q20_bases_before_filtering
q20_bases_after_filtering
q20_rate_before_filtering
q20_rate_after_filtering
q30_bases_before_filtering
q30_bases_after_filtering
q30_rate_before_filtering
q30_rate_after_filtering
gc_content_before_filtering
gc_content_after_filtering
adapter_trimmed_reads
adapter_trimmed_bases