v2.3.4

salmon 2.3.4

A bug-fix release on 2.3.3. It fixes a single-end handling bug in
alignment mode (salmon quant -a). Paired-end workflows, mapping-based
(reads) quantification, and single-end runs with --libType U are unaffected
and produce identical results. No index rebuild is required.

Fix: single-end alignment inputs are dropped under stranded library types (#1057)

In alignment mode, salmon classified each lone aligned record using only the
BAM 0x40 (first-in-pair) flag, and never consulted 0x1 ("template has
multiple segments" / paired). A genuine single-end read sets none of 0x1,
0x40, or 0x80, so it was mislabeled as a paired-end right orphan rather
than single-end. Under a stranded single-end library type (--libType SF or
SR) that pseudo-orphan classification can never satisfy the single-end
strandedness check, so every alignment was discarded and salmon reported
0 fragments mapped. --libType U was the only setting that worked, because it
accepts either orientation unconditionally.

The fix (#1058) keys the
single-end vs. orphan decision on the 0x1 flag, per the SAM/BAM
specification: a record with 0x1 unset is treated as genuine single-end, and
its own alignment strand (0x10) is what the strand filter uses. A record that
is part of a pair but reported alone (a true orphan) is still classified
left/right by 0x40, unchanged.

After the fix, single-end alignment inputs quantify correctly under all three
single-end library types:

• --libType SR accepts reverse-strand reads (BAM flag 16),
• --libType SF accepts forward-strand reads (flag 0),
• --libType U accepts both (unchanged).

This matches the behavior of the mapping-based (reads) path and the internal
genome-projection path, both of which already classified single-end reads
correctly.

Upgrading

Drop-in from 2.3.3: no index rebuild. Results are unchanged for paired-end
inputs, reads-mode quantification, and single-end --libType U. If you feed a
single-end transcriptomic BAM/SAM with a stranded library type (SF/SR),
salmon now quantifies it correctly instead of reporting 0 fragments mapped.

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Install salmon-cli 2.3.4

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/salmon/releases/download/v2.3.4/salmon-cli-installer.sh | sh

Download salmon-cli 2.3.4

File	Platform	Checksum
salmon-cli-aarch64-apple-darwin.tar.xz	Apple Silicon macOS	checksum
salmon-cli-x86_64-apple-darwin.tar.xz	Intel macOS	checksum
salmon-cli-aarch64-unknown-linux-gnu.tar.xz	ARM64 Linux	checksum
salmon-cli-x86_64-unknown-linux-gnu.tar.xz	x64 Linux	checksum