| name | salmon |
| description | Fast quantification of gene/transcript abundance; use --meta for metagenomes. Use this skill when working with salmon: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/COMBINE-lab/salmon. For routing across tools, use tool-selection. For end-to-end pipelines, use metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["quantification","abundance"] |
| upstream | https://github.com/COMBINE-lab/salmon |
Salmon
Upstream: COMBINE-lab/salmon
Citation
Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417–419 (2017). https://doi.org/10.1038/nmeth.4197
See also docs/references.md.
Analytical thinking
Quantify a non-redundant gene catalogue (nucleotides) with dehosted PE reads.
Typical catalogue path:
prodigal (contigs) → cd-hit | mmseqs2 (NR) → salmon quant --meta
→ eggnog-mapper on NR proteins
For metagenomes pass --meta. Prefer TPM vs counts consciously — downstream
stats must match the unit. CoverM genome abundance ≠ gene catalogue TPM.
Note: salmon 2.x (Rust) changed index format — rebuild indexes when upgrading;
bioconda may still ship 1.x (salmon-cpp). Pin and document the version.
How to run
salmon index -t NR/nucleotide.fa -i temp/salmon/index -p 8
salmon quant -i temp/salmon/index -l A -p 8 --meta \
-1 temp/hr/${id}_1.fastq -2 temp/hr/${id}_2.fastq \
-o temp/salmon/${id}.quant
salmon quantmerge --quants temp/salmon/*.quant -o result/salmon/gene.TPM
salmon quantmerge --quants temp/salmon/*.quant --column NumReads \
-o result/salmon/gene.count
Key parameters
| Flag | Notes |
|---|
--meta | Metagenome mode — required for community catalogues |
-l A | Auto library type; verify if stranded protocols used |
| Index | Rebuild after salmon major version change |
Decision tree
Abundance need?
├─ NR gene catalogue → salmon --meta
├─ Genome/MAG relative abundance → coverm
├─ Pathway/gene families from reads → humann
└─ Contig coverage for binning → coverm contig / mapper depths
Related skills
prodigal · cd-hit · mmseqs2 · eggnog-mapper · coverm · kneaddata ·
humann · tool-selection
