Command-line interface

salmon is invoked as salmon <command> [options]. Run salmon <command> --help for the authoritative, version-specific option list; this page summarizes the main commands and options.

salmon <command>

Commands:
  index       Build a salmon index from a transcriptome FASTA
  quant       Quantify transcript abundances from FASTQ reads (or a BAM)
  quantmerge  Merge a column across samples' quant files into a matrix
  debug-map   Diagnostic: per-read best-mapping detail
  alevin      Single-cell (removed; redirects to alevin-fry)

Global: -q/--quiet, -h/--help, -V/--version. --no-version-check is accepted for C++ compatibility and is a no-op (2.0 never checks for updates).

salmon index

Build a reusable index from one or more transcriptome FASTA files.

Option	Description
-t, --transcripts <FASTA>…	Transcript FASTA file(s). Required.
-i, --index <DIR>	Output index directory. Required.
-k, --kmerLen <N>	K-mer length (odd, ≤ 31 recommended). Default 31.
-m, --minimizerLen <N>	Minimizer length (0 = auto → 19 for the default k=31). Default 0.
-p, --threads <N>	Worker threads (0 = all cores). Default 0.
-d, --decoys <FILE>	File of decoy sequence names (one per line; decoy records must come last in the FASTA).
--keepDuplicates	Retain exact-duplicate transcript sequences instead of collapsing them.
-n, --no-clip	Don’t clip poly-A tails. By default a reference ending in ≥10 As has its trailing As trimmed (all-A references are dropped), matching pufferfish.
--gencode	GENCODE references: truncate each name at the first |.
--keepFixedFasta	Keep the cleaned (non-ACGT-replaced) reference FASTA.
--keepIntermediate	Keep intermediate compacted-dBG files.
--tmpdir <DIR>	Directory for build intermediates.
--filterSize <N>	Accepted for compatibility; no effect.

salmon index -t transcripts.fa -i salmon_index -p 16

salmon quant

Quantify from FASTQ reads (reads mode, -i), from a transcriptome BAM (alignment mode, -a), or from a RAD file of mappings (RAD mode, --rad).

Inputs / outputs

Option	Description
-i, --index <DIR>	Salmon index (reads mode).
-a, --alignments <BAM>	Alignment mode: a name-grouped BAM of reads aligned to the transcriptome. With --annotation, a genome-aligned BAM instead (see below).
--annotation <GTF|GFF>	Genome-alignment mode: project a genome-aligned BAM into transcriptome coordinates via this annotation. See genome-alignment quantification.
--genome <FASTA>	Genome FASTA (genome mode); enables bias correction by reconstructing transcript sequences from exon slices.
--juncMissDiscount <f>	Penalty for an unannotated splice junction in genome projection (default 1.0 = none).
--rad <RAD>	RAD mode: quantify a RAD file of mappings (salmon --writeRad or piscem map-bulk/sketch output) directly. No -i needed — reference names travel in the RAD header. See RAD I/O & deterministic quantification.
-t, --targets <FASTA>	Transcriptome FASTA (alignment mode). Enables the error model in ordinary alignment mode; supplies reference sequences for bias correction and (with --errorModel) the deterministic error model.
-l, --libType <TYPE>	Library type (e.g. IU, ISR, A for auto). Default A. See library types.
-1/-2, --mates1/2 <FASTQ>…	Paired-end read files.
-r, --unmatedReads <FASTQ>…	Single-end read files.
-o, --output <DIR>	Output directory. Required.
-p, --threads <N>	Worker threads (0 = all cores).
-g, --geneMap <FILE>	Transcript-to-gene map (GTF/GFF or 2-column TSV); also writes quant.genes.sf.

Mapping

Option	Description
--sketch	Alignment-free pseudoalignment path.
--sketchStrictOrphans	Strict orphan rule in sketch mode.
--allowDovetail	Admit dovetailed short-insert fragments.
--minScoreFraction <f>	Min alignment score as a fraction of perfect. Default 0.65.
--ma/--mp/--go/--ge	Match score / mismatch / gap-open / gap-extend.
--orphanChainSubThresh <f>	Orphan chain pruning (default 0.0 = align all).
--noErrorModel	Disable the alignment error model (ordinary alignment mode).
--errorModel	Opt in to the order-independent error model in deterministic alignment mode (-a --deterministic, needs -t). Off by default — deterministic mode scores by the BAM AS tag (single pass, at least as accurate against truth); this adds a second BAM pass. See deterministic alignment mode.

Model & bias

Option	Description
--seqBias	Sequence-specific bias correction.
--gcBias	Fragment-GC bias correction.
--posBias	Positional bias correction.
--noLengthCorrection	Use raw reference length (no effective-length correction).

RAD I/O & determinism

See the RAD I/O & deterministic quantification guide.

Option	Description
--writeRad <FILE>	Write per-fragment mappings to a RAD file (piscem map-bulk-compatible). Quantification still runs unless --skipQuant.
--skipQuant	Skip quantification (EM, Gibbs/bootstrap, quant.sf); still map, build equivalence classes, detect library type, write metadata.
--deterministic	Reproducible reads-mode quantification: map once to an intermediate RAD, then quantify from it with a fixed fragment-length distribution. Byte-identical across runs and thread counts.
--keepRad	Keep the --deterministic intermediate RAD (deleted by default).
--radCompress <CODEC>	RAD chunk compression for --writeRad / --deterministic: lz4 (default), zstd (smaller), or none.
--noCompressRad	Write uncompressed RAD chunks (overrides --radCompress).

Inference

Option	Description
--useEM	Standard EM instead of VBEM.
--meta	Metagenomic preset: plain EM, no range-factorized eq-classes, uniform init. Overrides --useEM/--rangeFactorizationBins.
--rangeFactorizationBins <N>	Range-factorization bins (0 disables). Default 4.
--numBootstraps <N>	Bootstrap replicates for posterior uncertainty.
--numGibbsSamples <N>	Gibbs posterior samples (mutually exclusive with bootstraps).
--thinningFactor <N>	Gibbs thinning factor. Default 16.
--incompatPrior <f>	Prior weight for strand-incompatible mappings. Default 0.

Diagnostics

Option	Description
--dumpEq / --dumpEqWeights	Dump equivalence classes (with weights).
--writeUnmappedNames	Write unmapped fragment names.
-z, --writeMappings <FILE>	Write per-mapping SAM records.

salmon quant -i salmon_index -l A -1 r1.fq.gz -2 r2.fq.gz -p 16 -o out

salmon quantmerge

Merge a chosen column (e.g. NumReads or TPM) across multiple samples’ quant.sf files into a single matrix.

Note

Coming from C++ salmon? See what changed in 2.0 for removed, renamed, and accepted-but-ignored options.