Version Compatibility

Reference examples tested with: BWA 0.7.17+, QUAST 5.2+, minimap2 2.26+, 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.

Assembly Polishing

"Polish my genome assembly" → Iteratively correct base-level errors in a draft assembly using short-read or long-read alignments.

• CLI: pilon --genome draft.fa --frags short_reads.bam (short-read), medaka_polish (ONT), racon (long-read)

Polishing Strategies