Sequencing QC

Platform-specific dashboards for monitoring sequencing run quality across Illumina, Oxford Nanopore, and PacBio instruments.

Overview

Libre Biotech includes dedicated QC dashboards for each major sequencing platform. These dashboards provide per-run quality metrics, sample tracking, and instrument performance monitoring. QC data can be linked to ISA samples for end-to-end provenance.

IlluminaQC

The Illumina dashboard tracks runs from MiSeq, NextSeq, NovaSeq, and other Illumina instruments.

Key metrics

Total reads, reads passing filter, % Q30
Cluster density and % clusters passing filter
Per-lane and per-sample yield
Index assignment and demultiplexing summary
InterOp metrics (intensity, focus, error rate by cycle)

Run views

Run list — All runs with status, instrument, date, read configuration
Run detail — Full metrics, sample table, lane-by-lane breakdown
Instrument summary — Performance trends per instrument

NanoporeQC

The Nanopore dashboard tracks runs from MinION, GridION, and PromethION devices.

Key metrics

Total bases, read count, N50 read length
Mean and median quality scores
Pore occupancy and throughput over time
Per-barcode demultiplexing summary
Flow cell utilisation

PacBioQC

The PacBio dashboard tracks SMRT cells from Sequel and Revio instruments.

Key metrics

CCS reads, HiFi reads, mean CCS quality
Polymerase read length and insert size distribution
Loading and productivity metrics
Per-barcode demultiplexing (Lima summary)

Linking QC data to ISA

QC runs can be linked to ISA sequencing processes to create a provenance chain from sample preparation through to quality assessment:

Navigate to a sequencing process
Go to the QC tab
Click Search QC Runs and select the platform (Illumina, Nanopore, or PacBio)
Search by run name, date, or instrument
Select the matching run
Map QC samples to ISA samples (match by name or manual selection)

Once linked, the process page displays QC metrics alongside the ISA metadata, and sample pages show their QC results.

Access control

QC dashboards require authentication. Access is controlled by project folder links:

Admin users see all runs and samples
Non-admin users see only runs linked to their group's project folders

Instrument management: Platform administrators can manage instruments and their metadata from the Instruments page, accessible via Docs → Instruments & QC.