LongBarcodeQC¶

LongBarcodeQC is a command-line tool for analyzing combinatorial barcode libraries sequenced with Oxford Nanopore long reads. It aligns reads to a reference plasmid, extracts the multi-cloning site (MCS) region, scores each read against a barcode library, and generates an interactive HTML summary report.

Features¶

• Merges and preprocesses FASTQ input
• Aligns reads to a reference plasmid using minimap2
• Extracts the MCS region from each read using flanking sequence anchors (parasail Smith-Waterman)
• Scores each read against a barcode library and calls the best-matching barcode per position
• Detects restriction enzyme cut sites within the MCS
• Generates a self-contained HTML report with interactive plots (read length distributions, barcode heatmaps, z-score distributions, restriction site summaries)
• Outputs a compressed summary CSV with per-read barcode calls and QC metrics

Quick links¶

• Installation
• Quickstart
• CLI Reference