Version Compatibility

Reference examples tested with: Salmon 1.10+, fastp 0.23+, kallisto 0.50+, pandas 2.2+

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.

Alignment-Free Quantification

"Quantify gene expression without alignment" → Estimate transcript abundances directly from FASTQ reads using pseudo-alignment or selective alignment, bypassing genome mapping.

• CLI: salmon quant -i index -l A -1 R1.fq.gz -2 R2.fq.gz -o quant/, kallisto quant -i index -o output R1.fq.gz R2.fq.gz

Quantify transcript abundance directly from FASTQ reads using pseudo-alignment (kallisto) or selective alignment (Salmon).

Salmon Workflow