NanoOK

NanoOK provides quality control and error profiling for Oxford Nanopore MinION sequencing data by producing tabular and graphical reports that summarize error profiles, quality metrics, and yield statistics for genomics, metagenomics, and transcriptomics analyses.

Key Features:

• Comprehensive Quality Control: Generates extensive tabular and graphical outputs and a multi-page PDF report detailing error profiles, quality metrics, and yield statistics.
• Multi-Reference Capability: Supports multi-reference analysis for metagenomic samples or multiplexed datasets involving multiple reference genomes.
• Support for Multiple Aligners: Compatible with four popular Nanopore aligners and designed for extensibility to incorporate additional aligners.
• Open-Source Implementation: Implemented in Java with supporting R scripts to permit customization and integration into bioinformatics workflows.
• Cross-Platform Compatibility: Tested on Linux and Mac OS X platforms.

Scientific Applications:

• Genomics: Quality control and error profiling of MinION reads to assess sequencing accuracy for genomic analyses.
• Metagenomics: Multi-reference and error-profiling capabilities to characterize complex microbial community sequencing datasets.
• Transcriptomics: Assessment of MinION transcriptome sequencing data through quality metrics and error profiles.
• Multiplexed and Multi-sample Experiments: Support for multi-reference analysis and multiple aligners to aid analysis of multiplexed or multi-sample studies.

Methodology:

NanoOK processes MinION base-calling output by extracting FASTA/FASTQ formatted data, supports multi-reference analysis, is compatible with four Nanopore aligners, and generates tabular and graphical outputs and a multi-page PDF report with error profiles, quality metrics, and yield statistics; the implementation uses Java with supporting R scripts and a modular design for pipeline integration.