Version Compatibility

Reference examples tested with: BUSCO 5.5+, BWA 0.7.17+, Flye 2.9+, QUAST 5.2+, SPAdes 3.15+, fastp 0.23+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Genome Assembly Pipeline

"Assemble and polish a genome from my sequencing reads" → Orchestrate read QC, assembly (hifiasm, Flye, SPAdes), polishing (Medaka, Pilon), scaffolding, contamination detection (BlobToolKit), and quality assessment (QUAST, BUSCO).

Complete workflow from sequencing reads to polished, quality-assessed genome assembly.

Workflow Overview