Routine Sequence QC

A generic pipeline that can be run routinely on all Illumina sequence runs, regardless of the project or organism of interest.

• Sequence quality information
• Possible contamination

Analyses

• Parse run-level QC statistics from the 'InterOp' directory and write to .csv and .json format.
• FastQC: sample-level sequence quality metrics
• mash: Estimate genome size and depth of coverage
• seqtk fqchk: Measure average sequence quality score, percent of bases above Q30 and GC content.
• kraken2 + bracken: Taxonomic classification of reads. Estimation of relative abundances of taxonomic groups (genus, species) in each sample.
• MultiQC: Collect several QC metrics into a single interactive HTML report.

Usage

nextflow run BCCDC-PHL/routine-sequence-qc \
  [--instrument_type nextseq] \
  [--kraken2_db /path/to/kraken2_db] \
  [--bracken_db /path/to/bracken_db] \
  [--seqtk_fqchk_threshold <threshold>] \
  [--mash_sketch_kmer_size <kmer_size>] \
  [--mash_sketch_minimum_copies <copies>] \
  --run_dir <your illumina run directory> \
  --outdir <output directory>

Outputs

<outdir>
├── abundance_top_n
│   ├── top_3_abundances_genus.csv
│   └── top_5_abundances_species.csv
├── basic_qc_stats
│   └── basic_qc_stats.csv
├── bracken
│   ├── <sample_id>_Genus_bracken_abundances.tsv
│   ├── <sample_id>_Genus_bracken_abundances_adjusted.tsv
│   ├── <sample_id>_Genus_bracken.txt
│   ├── <sample_id>_Genus_bracken_adjusted.txt
│   ├── <sample_id>_Species_bracken_abundances.tsv
│   ├── <sample_id>_Species_bracken_abundances_adjusted.tsv
│   ├── <sample_id>_Species_bracken.txt
│   ├── <sample_id>_Species_bracken_adjusted.txt
│   ├── ...
├── fastqc
│   ├── <sample_id>_R1_fastqc
│   ├── <sample_id>_R2_fastqc
│   ├── ...
├── interop_summary
│   ├── interop_index-summary.csv
│   ├── interop_summary.csv
│   └── interop_summary.json
├── kraken2
│   ├── <sample_id>_kraken2.txt
│   ├── ...
├── mash_sketch
│   ├── <sample_id>_R1_mash_sketch.txt
├── mash_sketch_summary
│   └── mash_sketch_summary.csv
├── multiqc
│   ├── multiqc_data
│   └── multiqc_report.html
└── parse_sample_sheet
│   └── sample_sheet.json
├── pipeline_complete.json
├── seqtk_fqchk
│   ├── <sample_id>_seqtk_fqchk_all_positions.csv
│   ├── <sample_id>_seqtk_fqchk_by_position.csv
└── seqtk_fqchk_summary
    └── seqtk_fqchk_summary.csv