Version Compatibility

Reference examples tested with: BUSCO 5.5+, QUAST 5.2+

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

• Python: pip show <package> then help(module.function) to check signatures
• 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.

HiFi Assembly

"Assemble a genome from HiFi reads" → Build a phased, reference-quality diploid assembly from PacBio HiFi reads with optional trio or Hi-C phasing for full haplotype resolution.

• CLI: hifiasm -o output reads.fq.gz

Basic Assembly

Goal: Produce a primary contig assembly from PacBio HiFi reads.