Version Compatibility

Reference examples tested with: Bowtie2 2.5.3+, STAR 2.7.11+, cutadapt 4.4+, numpy 1.26+

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

• Python: pip show <package> then help(module.function) to check signatures
• 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.

Ribo-seq Pipeline

"Analyze my ribosome profiling data from FASTQ to translation efficiency" → Orchestrate adapter trimming, rRNA depletion, genome alignment, periodicity QC, ORF detection (RiboCode), stalling analysis, and translation efficiency estimation (riborex).

Pipeline Overview