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QC Metrics Wiki

This document describes the Quality Control (QC) metrics generated and summarized in the QCD pipeline. The summary table is output as {prefix}_QC_summary.csv and integrates results from multiple steps in the workflow.

Input Data Sources

The summary function merges the following data sources:

• Coverage: Read coverage statistics per sample.
• MLST: Multi-locus sequence typing results.
• MultiQC FastQC: Raw and trimmed read quality metrics.
• QUAST: Assembly quality metrics (N50, total length).
• Contig distribution: Number of contigs per sample.
• Skani: Closest reference genome and species assignment.
• Genome size table: Reference genome sizes for length checks.
• Failed samples: Optionally, samples that failed coverage or assembly.

Output Columns

Column Name	Description
Sample	Sample identifier.
Total_reads	Total number of reads for the sample.
Total_bp	Total number of base pairs sequenced.
MeanReadLength	Mean read length.
Coverage	Estimated genome coverage (X).
Scheme	MLST scheme used.
ST	Sequence type (from MLST).
After_trim_per_base_sequence_content	Per-base sequence content after trimming.
After_trim_overrepresented_sequences	Overrepresented sequences after trimming.
After_trim_%GC	GC content (%) after trimming.
After_trim_Total Bases	Total number of bases after trimming.
After_trim_Total Sequences	Total number of sequences after trimming.
After_trim_median_sequence_length	Median sequence length after trimming.
After_trim_avg_sequence_length	Average sequence length after trimming.
After_trim_total_deduplicated_percentage	Percentage of deduplicated sequences after trimming.
After_trim_Sequence length	Sequence length after trimming.
After_trim_adapter_content	Adapter content after trimming.
N50	N50 value from assembly (length at which 50% of the assembly is contained in contigs of this length or longer).
Total length	Total length of the assembly.
Total # of contigs	Total number of contigs in the assembly.
QC Check	Final QC status for the sample (PASS/FAIL/Run FAIL).
ANI	Average Nucleotide Identity to closest reference (from Skani).
Align_fraction_ref	Fraction of reference genome aligned.
Align_fraction_query	Fraction of query genome aligned.
Ref_name	Closest reference genome name.
Species	Species assignment based on reference.

QC Check Logic

A sample is marked as FAIL if any of the following conditions are met:

• Total # of contigs > max_contigs (from config)
• Total # of contigs < min_contigs (from config)
• Coverage < coverage (from config)
• Assembly length is not within ±15% of the expected species genome size
• Missing contig or assembly length information

Otherwise, the sample is marked as PASS.

Additional Notes

• The summary table may include samples that failed coverage or assembly steps, with missing values filled as "NA".

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For more details, see the summary function in QCD_report.smk.