long-read-genomics

What problem does it solve?

Nanopore and PacBio long-read projects require integrated QC, alignment, polishing, methylation-aware analysis, and structural variant discovery across datasets. This skill provides an end-to-end blueprint to streamline these steps and ensure reproducible results.

Core Features & Use Cases

• QC & quality metrics: Evaluate read length distributions, accuracy, and platform-specific artifacts for reliable downstream analyses.
• Alignment & polishing: Perform methylation-aware alignment and polishing to improve consensus accuracy and variant calling reliability.
• Variant discovery: Generate summaries for structural variants and small variants from long-read data.
• Use Case: Apply this skill to a project with a nanopore dataset to obtain aligned reads, polished assemblies, and variant reports suitable for downstream interpretation.

Quick Start

Process raw long-read data to produce aligned reads, polished assemblies, and variant summaries against a reference genome.