Version Compatibility

Reference examples tested with: 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.

Bowtie2 Alignment

"Align DNA reads with Bowtie2" → Map short reads to a reference genome using Bowtie2's end-to-end or local alignment modes.

• CLI: bowtie2 -x index -1 R1.fq -2 R2.fq | samtools sort -o aligned.bam

Build Index