Audit genomics experiment quality metrics
quality-assessmentskillsetup L2★35
ammawla/encode-toolkit ↗What it does
Evaluate genomics data quality across standard metrics
Best for
Quickly deciding if a sequencing sample meets publication standards without manual QC checklist.
Inputs
- · Sequencing data (BAM, FASTQ, or metrics table)
Outputs
- · Pass/fail assessment
- · Metric report (mapping rate, duplicates, coverage)
Requires
- · samtools
- · FastQC
- · Picard CollectMetrics
Preconditions
- · Reference genome
- · Minimum coverage threshold
Failure modes
- · Metrics below ENCODE cutoffs
- · Sample contamination not flagged
Trust signals
- · ENCODE/SEQC QC thresholds
- · Automated reporting