Riker

note

Fast Rust toolkit that ports key sequencing QC tools from Picard.

https://github.com/fulcrumgenomics/riker

Riker is a fast Rust toolkit for sequencing QC metrics that ports many of the most widely-used tools from Picard with cleaner output and better performance.

Supported subtools:

• alignment (equivalent to Picard's CollectAlignmentSummaryMetrics)
• basic (equivalent to CollectBaseDistributionByCycle, MeanQualityByCycle, and QualityScoreDistribution)
• gcbias (equivalent to CollectGcBiasMetrics)
• hybcap (equivalent to CollectHsMetrics)
• isize (equivalent to CollectInsertSizeMetrics)
• wgs (equivalent to CollectWgsMetrics)

Riker emits plain TSV files with sample as the first column and snake_case column names; this module parses those files directly. Per-target and per-base coverage outputs from hybcap (only emitted with --per-target-coverage) are not parsed in this version. The error subtool is also not yet supported.

Coverage thresholds

Riker emits cumulative coverage fractions for wgs (e.g. frac_bases_at_30x) and hybcap (e.g. frac_target_bases_30x). The threshold shown in the General Statistics table can be customised:

riker_config:
  general_stats_target_coverage:
    - 10
    - 30

File search patterns

riker/alignment:
  contents_re: ^sample\b.*\bcategory\b
  fn: '*.alignment-metrics.txt'
  num_lines: 1
riker/basic_base_dist:
  contents_re: ^sample\b.*\bfrac_a\b
  fn: '*.base-distribution-by-cycle.txt'
  num_lines: 1
riker/basic_mean_quality:
  contents_re: ^sample\b.*\bmean_quality\b
  fn: '*.mean-quality-by-cycle.txt'
  num_lines: 1
riker/basic_quality_dist:
  contents_re: ^sample\b.*\bfrac_bases\b
  fn: '*.quality-score-distribution.txt'
  num_lines: 1
riker/gcbias_detail:
  contents_re: ^sample\b.*\bnormalized_coverage\b
  fn: '*.gcbias-detail.txt'
  num_lines: 1
riker/gcbias_summary:
  contents_re: ^sample\b.*\bgc_0_19_normcov\b
  fn: '*.gcbias-summary.txt'
  num_lines: 1
riker/hybcap_metrics:
  contents_re: ^sample\b.*\bbait_territory\b
  fn: '*.hybcap-metrics.txt'
  num_lines: 1
riker/isize_histogram:
  contents_re: ^sample\b.*\bfr_count\b
  fn: '*.isize-histogram.txt'
  num_lines: 1
riker/isize_metrics:
  contents_re: ^sample\b.*\bpair_orientation\b
  fn: '*.isize-metrics.txt'
  num_lines: 1
riker/wgs_coverage:
  contents_re: ^sample\b.*\bbases_at_or_above\b
  fn: '*.wgs-coverage.txt'
  num_lines: 1
riker/wgs_metrics:
  contents_re: ^sample\b.*\bgenome_territory\b
  fn: '*.wgs-metrics.txt'
  num_lines: 1