Version Compatibility

Reference examples tested with: BUSCO 5.5+, BWA 0.7.17+, QUAST 5.2+, bedtools 2.31+, 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 Scaffolding

"Scaffold my contigs to chromosome level" → Order and orient contigs into chromosome-scale scaffolds using Hi-C proximity ligation data.

• CLI: yahs contigs.fa hic_alignments.bam, 3d-dna, salsa2

Hi-C Data Preprocessing

Goal: Prepare Hi-C read alignments for scaffolding tools.