long-read-genomics

Processing nanopore data for methylation-aware alignment and structural variant discovery requires a workflow that integrates QC, alignment, polishing, and variant calling against a reference genome to generate aligned files, polished consensus, and variant summaries.

Running QC and polishing PacBio long-read assemblies involves evaluating read length distributions and platform-specific artifacts first, then applying polishing to alignments to improve consensus accuracy and variant calling reliability.

You can use a single workflow for de novo assembly and structural variant calling in long-read genomics by specifying long-read data and sample metadata as inputs to generate polished assemblies and structural variant summaries simultaneously.

This long-read analysis approach handles platform-specific artifacts from nanopore and PacBio data by evaluating quality metrics and accuracy during the QC step to ensure reliable downstream alignments and variant discovery.

Generating a polished consensus sequence from raw long-read data requires performing initial QC, aligning reads to a reference genome, and applying a polishing step to correct errors and improve consensus accuracy.