ugbio-seq-qc 1.27.1

Ultima Genomics sequencing QC HTML reports

ugbio_seq_qc

Sequencing QC HTML reports for Ultima Genomics runs.

This package generates self-contained, plotly-based HTML QC reports from Sorter statistics output (the per-sample JSON/CSV files produced by the on-tool Sorter). It lives outside ugbio_core because it depends on ugbio_cloud_utils (cloud_sync) and boto3 for fetching inputs from S3 — dependencies that the dependency-free ugbio_core foundation must not carry.

Reports

• seq_qc_report — single-sample report. One sample's JSON + CSV → one HTML page with a summary table and coverage / read-length / base-quality / MAPQ figures.
• seq_qc_multi_sample_report — multi-sample report. Auto-discovers the real samples in a run (via the LibraryInfo sample sheet when present, otherwise by name pattern), then renders one figure per sample grouped by metric, plus a samples-as-rows / metrics-as-columns comparison table with frozen header row and first column.

Both accept a local directory or an s3:// URI.

Usage

# Single sample — explicit files or a directory to auto-detect the basename
seq_qc_report --json sample.json --csv sample.csv --output report.html
seq_qc_report --input-dir s3://.../603559-L13064-Z0152-CATGCAACACTAGAT/

# Multi-sample — a whole run directory (local or s3://)
seq_qc_multi_sample_report --run-dir s3://.../603559/ --output run_report.html

# Multi-sample — explicit per-sample directories
seq_qc_multi_sample_report --input-dir s3://.../sampleA/ --input-dir s3://.../sampleB/

Modules

Module	Role
seq_qc_report.py	Single-sample report: plotly figure builders (shared) + HTML assembly + CLI.
seq_qc_multi_sample_report.py	Multi-sample HTML assembly + comparison table + CLI; reuses the figure builders from seq_qc_report.
sample_discovery.py	Sample discovery: LibraryInfo XML parsing, name-pattern filtering, sample loading into SampleData.
file_resolution.py	Shared S3 / local file-resolution helpers (list_s3_dir, list_s3_subdirs, resolve_sample_files, ...).