DRAGEN

Description

Illumina DRAGEN is a Bio-IT Platform that provides ultra-rapid secondary analysis of sequencing data using field-programmable gate array technology (FPGA).

DRAGEN has a number of different pipelines and outputs, including base calling, DNA and RNA alignment, post-alignment processing and variant calling, covering virtually all stages of typical NGS data processing. For each stage, it generates QC files with metrics resembling those of samtools-stats, mosdepth, bcftools-stats and alike. This MultiQC module supports some of the output but not all.

• <output prefix>.wgs_fine_hist_<tumor|normal>.csv
  • Coverage distribution and cumulative coverage plots
• <output prefix>.mapping_metrics.csv
  • General stats table, a dedicated table, and a few barplots
• <output prefix>.wgs_coverage_metrics_<tumor|normal>.csv
  • General stats table and a dedicated table
• <output prefix>.qc-coverage-region-<1|2|3>_coverage_metrics.csv
  • General stats table and a dedicated table
• <output prefix>.wgs_contig_mean_cov_<tumor|normal>.csv
  • A histogram like in mosdepth, with each chrom as a category on X axis, plus a category for autosomal chromosomes average
• <output prefix>.fragment_length_hist.csv
  • A histogram plot
• <output prefix>.ploidy_estimation_metrics.csv
  • Add just Ploidy estimation into the general stats table
• <output prefix>.vc_metrics.csv
  • A dedicated table and the total number of Variants into the general stats table
• <output prefix>.gc_metrics.csv
  • A histogram and summary statistics table on GC content metrics
• <output prefix>.trimmer_metrics.csv
  • A summary table of tirmmer metrics
• <output prefix>.time_metrics.metrics
  • A bar graph of the total run time and a breakdown of the run time of each individual step
• <output prefix>.quant.metrics.csv
  • A bar graph of RNA fragments
• <output prefix>.quant.transcript_coverage.txt
  • A line plot of average coverage along RNA transcripts
• <output prefix>.scRNA.metrics.csv or <output prefix>.scRNA_metrics.csv
  • Summary table for single-cell RNA metrics
• <output prefix>.scATAC.metrics.csv or <output prefix>.scATAC_metrics.csv
  • Summary table for single-cell ATAC metrics

Each QC output adds a section into the report if a corresponding QC file is found.

File search patterns

dragen/vc_metrics:
  fn: "*.vc_metrics.csv"
dragen/gvcf_metrics:
  fn: "*.gvcf_metrics.csv"
dragen/ploidy_estimation_metrics:
  fn: "*.ploidy_estimation_metrics.csv"
dragen/wgs_contig_mean_cov:
  fn_re: .*\.wgs_contig_mean_cov_?(tumor|normal)?\.csv
dragen/overall_mean_cov_metrics:
  fn_re: .*_overall_mean_cov.*\.csv
dragen/coverage_metrics:
  fn_re: .*_coverage_metrics.*\.csv
dragen/wgs_fine_hist:
  fn_re: .*\.wgs_fine_hist_?(tumor|normal)?\.csv
dragen/fragment_length_hist:
  fn: "*.fragment_length_hist.csv"
dragen/mapping_metrics:
  fn: "*.mapping_metrics.csv"
  contents: Number of unique reads (excl. duplicate marked reads)
  num_lines: 50
dragen/gc_metrics:
  fn: "*.gc_metrics.csv"
dragen/trimmer_metrics:
  fn: "*.trimmer_metrics.csv"
dragen/time_metrics:
  fn: "*.time_metrics.csv"
dragen/rna_quant_metrics:
  fn: "*.quant[._]metrics.csv"
dragen/rna_transcript_cov:
  fn: "*.quant.transcript_coverage.txt"
dragen/sc_rna_metrics:
  fn: "*.scRNA[._]metrics.csv"
dragen/sc_atac_metrics:
  fn: "*.scATAC[._]metrics.csv"
dragen_fastqc:
  fn: "*.fastqc_metrics.csv"