Version Compatibility

Reference examples tested with: QUAST 5.2+, BUSCO 5.5+ (and 6.x for odb12 lineages), compleasm 0.2.6+, Merqury 1.3+, meryl 1.4+, minimap2 2.26+, Inspector 1.2+, CRAQ 1.0+, merfin 1.0+, GenomeScope2 2.0+.

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

• CLI: <tool> --version then <tool> --help to confirm flags
• Python: pip show <package> then help(module.function) to check signatures

Results depend on inputs that outlive the binary version - record them:

• BUSCO/compleasm depend on the lineage dataset and OrthoDB generation. _odb10 (BUSCO 5) and _odb12 (BUSCO 6 default) gene sets are not comparable across the version boundary; a 99% on the shallow eukaryota_odb10 (~255 genes) is a different claim from 99% on a deep clade set (~5,500+).
• Merqury QV/completeness depend on the k-mer size (from best_k.sh <genome_size>, not hardcoded) and the read set used for the k-mer DB (use accurate reads; see the circularity warning below).
• NG50/NGx/auNG depend on the expected genome-size estimate (GenomeScope2 / flow cytometry / a congener).

If code throws an error, introspect the installed tool and adapt rather than retrying.

Assembly QC

"Is my genome assembly any good?" -> Measure all three orthogonal axes - contiguity, completeness, correctness - with reference-free methods, because no single number (least of all N50) is quality.

• CLI: quast.py asm.fa --large --eukaryote -o out (contiguity + reference-based structure), busco -i asm.fa -m genome -l <lineage> or compleasm run -a asm.fa -l <lineage> (gene completeness), merqury.sh reads.meryl asm.fa out (reference-free QV + k-mer completeness), inspector.py -c asm.fa -r reads.fq (reference-free structural errors)