domains / families / science / bio-longread-medaka

bio-longread-medaka

separate

Polish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific basecaller versions. Use when improving ONT-only assemblies or calling variants from Nanopore data without short-read polishing.

When to use

• improving ONT-only assemblies
• calling variants from Nanopore data
• polishing assemblies without short-read polishing
• haploid variant calling
• polishing specific regions
• multiple rounds of polishing
• calling variants from existing BAM

When not to use

• diploid variant calling
• short-read variant calling

Skill page

Source