What changed in 2.0

salmon 2.0 is a from-scratch Rust rewrite. It keeps the same core workflow (salmon index → salmon quant → quant.sf) and the same output formats downstream tools consume, but it is a new major version and makes some breaking changes. This page maps C++ options and behavior to 2.0.

Breaking change: rebuild your index

Rebuild required

2.0 uses a new index format and cannot read C++ (pufferfish) indices. Rebuild with salmon index from 2.0. Loading a C++ index — or pointing C++ salmon at a 2.0 index — is detected and rejected with a clear error.

quant.sf is unchanged (drop-in for tximport/tximeta). Inferential replicates (aux_info/bootstrap/… for both --numBootstraps and --numGibbsSamples) are written in the same format C++ salmon used, so tximport/fishpond/swish keep working. The bias-model diagnostic dumps in aux_info/ are in a documented Rust format (see the output format specification); they are not consumed by the standard downstream R packages.

Removed subcommands

C++	2.0
salmon alevin	Removed. Use the alevin-fry ecosystem for single-cell. salmon alevin … prints a redirect and exits.

Removed options

Passing any of these errors out with a pointer to this guide. They are gone because the underlying feature was removed or has no equivalent in 2.0.

Option	Subcommand	Why / alternative
--features	index	Index-feature dump not supported by the cf1-rs/piscem-rs index builder.
--mimicBT2, --mimicStrictBT2	quant	bowtie2-mimicking presets removed; selective alignment is the single supported mode.
--minAssignedFrags	quant	The “zero the output below N assigned fragments” guard was removed; 2.0 reports what it quantifies.
--alternativeInitMode, --bootstrapReproject, --noGammaDraw	quant	Inference-internal toggles not present in the 2.0 optimizer/Gibbs implementation.
--numBiasSamples	quant	2.0 collects bias samples online (abundance-aware, dual-phase), so a fixed sample budget no longer applies.
--auxTargetFile, --writeOrphanLinks	quant -a	Removed alignment-mode features.

Accepted but ignored

These still parse so existing scripts run; 2.0 logs a warning and ignores them (the behavior is either the default now or handled differently).

• index: --filterSize
• quant: --eqclasses, --noFragLengthDist, --noSingleFragProb, --mismatchSeedSkip, --disableChainingHeuristic, --hitFilterPolicy, --maxRecoverReadOcc, --validateMappings (selective alignment is the default)
• quant -a: --mappingCacheMemoryLimit, -s/--sampleOut, -u/--sampleUnaligned, --writeQualities

New in 2.0

• --sketch — alignment-free pseudoalignment mode (faster). See mapping modes.
• --sketchStrictOrphans — in --sketch, only orphan a pair when the other mate had no matching k-mers at all (the conservative rule). The default is the relaxed rule, which tracks selective alignment more closely.
• --allowDovetail — now honored in --sketch as well.
• --ignoreTxVersion — compare -g/--geneMap identifiers without their trailing .N version suffix, as tximport’s option of the same name does. Off by default. See Ensembl cDNA + GTF.

Behavior differences to be aware of

• Sketch orphan rule defaults to the relaxed policy (see --sketchStrictOrphans).
• -g/--geneMap: unmatched transcripts are reported differently, not aggregated differently. As in C++ salmon’s aggregateEstimatesToGeneLevel, a transcript with no gene-map entry is emitted as its own single-transcript gene, named after the transcript, so nothing quantified is dropped on the way to gene level and tximport can apply its own transcript-to-gene policy to the whole file. What changed is the reporting: C++ warned once per unmatched transcript (half a million lines on a failed join), while 2.x warns once with the count and writes the names to aux_info/genemap_unmatched_txps.json, under an unmatched_transcripts key. That file is removed when nothing is unmatched, so its presence always refers to the current run. 2.x additionally warns when the match rate is at or below 50%, says how many transcripts would match without the version suffix, and names --ignoreTxVersion. A quant.genes.sf whose rows are mostly stand-ins is transcript-level output under a gene-level file name; the run’s closing line says so explicitly when any row is a stand-in.
• Selective-alignment chain pruning: 2.0 defaults --orphanChainSubThresh and --postMergeChainSubThresh to 0.0 (off) — it aligns every candidate, marginally more sensitive than C++ (0.95 / 0.9). Quantification is essentially unaffected (per-transcript Pearson ≈ 0.999); pass --orphanChainSubThresh 0.95 --postMergeChainSubThresh 0.9 to reproduce C++ mapping counts exactly.

-p on compressed input

-p is accepted unchanged, but from 2.5.0 it names one execution-slot budget shared between mapping and gzip decompression, rather than a mapping-thread count with decompression taken on top. C++ salmon (and 2.x before 2.5.0) could run more total threads than -p on compressed input; 2.5.0 stays within the budget and divides it from live measurement. Totals and results are unaffected; wall time on compressed input may differ from what the old accounting produced at the same -p. See threads and compressed input.

Unchanged

Index/quant basics, quant.sf, cmd_info.json, lib_format_counts.json, aux_info/meta_info.json, --libType/-l, --seqBias, --gcBias, --posBias, --numBootstraps, --numGibbsSamples, --useEM, --dumpEq, decoys, and salmon quantmerge.