Can I use custom reference genomes with this skill?

Yes, you can initialize a local registry and add custom FASTA files or automatically import standard references like GRCh38 and T2T.

What alignment tools does ONT Align support?

ONT Align primarily leverages minimap2 and dorado to perform high-performance alignment of Oxford Nanopore reads using specific presets like map-ont, lr:hq, and splice.

Does this skill help with data reproducibility?

Absolutely. It integrates with the ont-experiments framework to provide provenance tracking for all alignment tasks, ensuring researchers can trace the history of their data processing.

What alignment modes are available for edit distance calculations?

It supports Global alignment (Needleman-Wunsch), Semi-global (HW), and Infix (SHW) modes via the edlib library for versatile sequence comparison.

ONT Align

Name: ONT Align
Author: Single-Molecule-Sequencing

bySingle-Molecule-Sequencing

Data Science & ML

Automates Oxford Nanopore sequence alignment, reference genome management, and edit distance computations for genomic data analysis.

About

ONT Align is a specialized bioinformatics toolkit designed to streamline Oxford Nanopore Technologies (ONT) data workflows within Claude Code. It provides a robust interface for aligning long-read sequencing data using industry-standard tools like minimap2 and dorado, while managing a centralized registry for reference genomes such as GRCh38 and T2T. The skill excels at generating detailed BAM quality control metrics and computing high-performance Levenshtein edit distances using edlib. By integrating with the broader ont-experiments ecosystem, it ensures that every alignment and sequence comparison is performed with full provenance tracking, making it an essential tool for reproducible genomic research.

Key Features

Comprehensive BAM quality control, including coverage metrics and statistical reports
0 GitHub stars
High-performance read alignment using minimap2 and dorado with optimized presets
Fast Levenshtein edit distance computation via edlib for sequence comparison
Seamless integration with ont-experiments for automated provenance and experiment tracking
Centralized reference genome registry for managing FASTA files and standard builds

Use Cases

Aligning long-read ONT data to human reference genomes for variant discovery or structural analysis
Performing pairwise or all-vs-all sequence comparisons to benchmark similarity and edit distances
Managing and versioning reference genomes across large-scale bioinformatics pipelines

About

Key Features

Comprehensive BAM quality control, including coverage metrics and statistical reports
0 GitHub stars
High-performance read alignment using minimap2 and dorado with optimized presets
Fast Levenshtein edit distance computation via edlib for sequence comparison
Seamless integration with ont-experiments for automated provenance and experiment tracking
Centralized reference genome registry for managing FASTA files and standard builds

Use Cases

Aligning long-read ONT data to human reference genomes for variant discovery or structural analysis
Performing pairwise or all-vs-all sequence comparisons to benchmark similarity and edit distances
Managing and versioning reference genomes across large-scale bioinformatics pipelines