NanoporeInspect: An interactive tool for evaluating nanopore sequencing quality and ligation efficiency

Area of Science:

• Bioinformatics
• Molecular Biology
• Genomics

Background:

• Accurate ligation of artificial sequences (primers, adapters, barcodes) is critical for high-quality nanopore sequencing libraries, particularly in SELEX-based aptamer discovery.
• Ligation errors can lead to sequence misidentification and data loss, compromising downstream analysis.
• Current quality control tools lack specific features to evaluate the positioning and prevalence of these artificial sequences.

Purpose of the Study:

• To introduce NanoporeInspect, a novel web-based tool for assessing ligation efficacy and identifying systematic biases in nanopore sequencing data.
• To provide targeted quality control for artificial sequence ligation, enhancing library preparation for aptamer discovery.

Main Methods:

• Development of a user-friendly, web-based platform utilizing Flask, Celery, and Redis for scalable, asynchronous processing.
• Integration of Plotly for interactive data visualization.
• Evaluation of NanoporeInspect using diverse nanopore sequencing datasets.

Main Results:

• NanoporeInspect effectively differentiates between high and low ligation quality libraries.
• Inefficient ligation resulted in irregular adapter and barcode distributions, signaling preparation issues.
• High-quality libraries exhibited uniform adapter and barcode patterns, indicating successful ligation.

Conclusions:

• NanoporeInspect provides valuable insights into ligation efficiency, crucial for optimizing nanopore sequencing library preparation.
• The tool aids in identifying and rectifying systematic biases, improving the reliability of aptamer discovery and sequencing data.
• NanoporeInspect enhances quality control for nanopore sequencing, particularly in applications sensitive to ligation accuracy.