Alignment-Free Quantification

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

Salmon Workflow

Build Index

# Download transcriptome FASTA
# Ensembl: Homo_sapiens.GRCh38.cdna.all.fa.gz

# Basic index (fast, less accurate)
salmon index -t transcripts.fa -i salmon_index