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.

HISAT2 RNA-seq Alignment

"Align RNA-seq reads with HISAT2" → Map RNA-seq reads to a reference genome with splice-aware alignment. Suitable for gene expression quantification workflows.

• CLI: hisat2 -x index -1 R1.fq -2 R2.fq | samtools sort -o aligned.bam

Build Index