salmon

TAFFISH app for Salmon, a fast transcript-level RNA-seq quantification tool from COMBINE-lab.

Package Identity

Field	Value
name	salmon
command	taf-salmon
kind	tool
TAFFISH version	2.1.1-r1
container image	ghcr.io/taffish/salmon:2.1.1-r1
upstream	COMBINE-lab/salmon
upstream release	v2.1.1
runtime version	salmon 2.1.1
native platforms	linux/amd64, linux/arm64

What Is Included

This app packages the official Salmon v2.1.1 Rust CLI Linux release binaries:

• salmon-cli-x86_64-unknown-linux-gnu.tar.xz
  • SHA256: 184d87c5f376b33074e5d5a26538201d3ab13a9c7ea57c7862359b0c0d678d0e
• salmon-cli-aarch64-unknown-linux-gnu.tar.xz
  • SHA256: dea1432725e8530f90c75c0bcbbb8d7e88d145af23862aeecbbaa98bdb5f89fe

The Dockerfile selects the correct upstream asset from Docker TARGETARCH, verifies the checksum, installs the upstream salmon binary under /opt/salmon/salmon, and exposes it as /usr/local/bin/salmon.

Salmon 2 is a from-scratch Rust rewrite. It keeps the core salmon index -> salmon quant -> quant.sf workflow and downstream quantification table formats, but it is a new major version with intentional breaking changes.

The runtime image uses debian:13-slim and the official Linux GNU binary. The v2 binary is much lighter than the old C++ distribution and depends only on the standard GNU runtime libraries available in Debian 13, notably libgcc_s, libm, and libc.

Basic Usage

Show TAFFISH wrapper help:

taf-salmon --help

Show upstream Salmon help and version:

taf-salmon -- --help
taf-salmon -- --version
taf-salmon salmon --help
taf-salmon salmon --version

Build a Salmon 2 index:

taf-salmon salmon index \
  -t transcripts.fa \
  -i salmon_index \
  -k 31 \
  -p 8

Quantify single-end reads:

taf-salmon salmon quant \
  -i salmon_index \
  -l A \
  -r reads.fq.gz \
  -o sample_quant \
  -p 8

Quantify paired-end reads:

taf-salmon salmon quant \
  -i salmon_index \
  -l A \
  -1 reads_1.fq.gz \
  -2 reads_2.fq.gz \
  -o sample_quant \
  -p 8

Use the Salmon 2 sketch mode:

taf-salmon salmon quant \
  -i salmon_index \
  -l A \
  -r reads.fq.gz \
  --sketch \
  -o sample_sketch_quant \
  -p 8

Merge transcript TPMs from multiple quant.sf outputs:

taf-salmon salmon quantmerge \
  --quants sample1_quant sample2_quant \
  --names sample1 sample2 \
  --column TPM \
  -o merged_tpm.tsv

TAFFISH Command Mode

This is a normal TAFFISH tool app with command_mode = true.

For Salmon subcommands, prefer the explicit executable form:

taf-salmon salmon index ...
taf-salmon salmon quant ...
taf-salmon salmon quantmerge ...
taf-salmon salmon debug-map ...

Do not rely on:

taf-salmon index ...

In command mode, a non-option first argument can be interpreted as a container executable name rather than as a Salmon subcommand. The explicit taf-salmon salmon ... form is unambiguous and also lets users run the same container environment directly.

For option-leading arguments to the default upstream command, this also works:

taf-salmon -- --version
taf-salmon -- --help

Version Check And Network

Salmon 2 accepts --no-version-check and SALMON_NO_VERSION_CHECK for compatibility with C++ Salmon, but upstream documents them as no-ops: Salmon 2 does not contact the network for version checks. Keeping the flag in scripts is safe, but no longer necessary.

Functional Surface

Packaged upstream command:

• salmon index: build a Salmon 2 index from transcript FASTA
• salmon quant: quantify transcript abundance from reads or alignments
• salmon quant --sketch: use the Salmon 2 sketch / pseudoalignment path
• salmon quantmerge: merge Salmon quantification tables
• salmon debug-map: diagnostic per-read best-mapping detail
• salmon alevin: present only as an upstream migration message

Salmon 2 removed the legacy integrated salmon alevin implementation. This is an upstream change, not a TAFFISH packaging omission. Upstream recommends the piscem plus alevin-fry ecosystem for current single-cell workflows.

The old top-level salmon --cite command is not present in Salmon 2. Citation information remains documented upstream and below.

Compatibility Notes

Salmon 2.1.x writes an explicit Salmon index format version in info.json. This package still writes index_version = 1, matching Salmon 2.1.0. Rebuild all pre-2.1.0 indices before quantification; indices built by Salmon 2.1.0 are expected to remain compatible with this 2.1.1 package.

Downstream quantification outputs remain compatible: quant.sf, cmd_info.json, lib_format_counts.json, aux_info/meta_info.json, and inferential replicate outputs are intended to stay drop-in for tximport, tximeta, fishpond, and swish.

The Salmon 2 migration guide and v2.1.0 release notes document removed, accepted-but-ignored, and new options. Notable changes include:

• --sketch and --sketchStrictOrphans are new Salmon 2 quant options.
• --minAssignedFrags is removed.
• --features for index is removed.
• several niche C++ inference and alignment options are rejected or accepted only as compatibility no-ops.

Salmon 2.1.1 is a correctness-and-completeness patch over 2.1.0. Upstream highlights include corrected num_mapped reporting for stranded libraries, reworked handling of negligible abundance estimates with inference_truncated_mass metadata, inferential replicate output rows aligned with quant.sf, and bootstrap / Gibbs support in alignment mode. Standard point-estimate quant.sf output remains compatible with common downstream readers.

The preceding 2.1.0 release introduced the Salmon 2 index format marker, applied -l A library-type filtering, fixed concordant-pairing and anchored-alignment behavior, added default uni-MEM seeding, improved decoy-aware indexing and sketch-mode behavior, emitted duplicate_clusters.tsv under --keepDuplicates, and implemented fragment-length probability behavior around --noFragLengthDist.

The app supports native Linux amd64 and native Linux arm64 through official upstream binaries. No Docker platform emulation is required for either declared platform.

The container includes the upstream binary, upstream README and BSD-3-Clause license, GNU runtime libraries from Debian 13, and CA certificates. It does not bundle reference transcriptomes, genomes, decoy lists, annotation files, piscem, alevin-fry, simpleaf, oarfish, or external aligners.

Smoke Coverage

The smoke tests are independent and run without network access. They check:

• salmon 2.1.1 runtime version and Rust-port help banner
• no-op compatibility behavior for --no-version-check
• help for index, quant, quantmerge, and debug-map
• dynamic library resolution through ldd
• a tiny Salmon 2 index build that writes info.json, index.ssi, and index.ctab, and records index_version = 1
• a tiny single-end selective-alignment quant run that writes quant/quant.sf
• a tiny quant --sketch run that writes sketch_quant/quant.sf
• quantmerge on two synthetic quant.sf directories
• the upstream alevin removal and migration message

These tests verify packaging, command availability, and small real execution paths. They are not a substitute for biological validation on production references and read sets.

Upstream

• Upstream repository: https://github.com/COMBINE-lab/salmon
• Documentation: https://combine-lab.github.io/salmon/
• Release: https://github.com/COMBINE-lab/salmon/releases/tag/v2.1.1
• Migration guide: https://github.com/COMBINE-lab/salmon/blob/v2.1.1/MIGRATION.md
• Upstream license: BSD-3-Clause
• Citation: Patro et al. 2017, Nature Methods
• DOI: 10.1038/nmeth.4197
• PMID: 28263959