meryl

TAFFISH wrapper for Meryl, a genomic k-mer counter and sequence utility used by Merqury and related assembly-evaluation workflows.

This app packages upstream Meryl 1.4.1 from the official meryl-1.4.1.Linux-amd64.tar.xz release asset.

Release 1.4.1-r3 is a license-metadata TAFFISH update. It keeps the upstream software, Dockerfile, runtime dependencies, smoke tests, platform declaration, help text, and command behavior unchanged from 1.4.1-r2, while correcting the app/upstream license boundary.

Package metadata:

name: meryl
command: taf-meryl
version: 1.4.1-r3
kind: tool
image: ghcr.io/taffish/meryl:1.4.1-r3
upstream release: v1.4.1
upstream runtime version: meryl 1.4.1

Install

taf install meryl

Then run:

taf-meryl --help
taf-meryl --version
taf-meryl -- --version
taf-meryl meryl --version

taf-meryl --help shows TAFFISH wrapper help. Use -- when the first upstream argument starts with -, for example taf-meryl -- --version. Use command mode for commands inside the same container, for example taf-meryl meryl-lookup.

Commands

The container includes the public commands from the official Meryl Linux-amd64 binary release:

• meryl
• meryl-lookup
• meryl-import
• meryl-analyze
• meryl-simple
• position-lookup

The default command is meryl:

taf-meryl -- k=21 memory=64 threads=8 count reads.fastq.gz output reads.meryl
taf-meryl -- histogram reads.meryl > reads.hist
taf-meryl -- statistics reads.meryl > reads.stats
taf-meryl -- print reads.meryl > reads.kmers

The same calls can be written in explicit command mode:

taf-meryl meryl k=21 memory=64 threads=8 count reads.fastq.gz output reads.meryl
taf-meryl meryl histogram reads.meryl
taf-meryl meryl statistics reads.meryl
taf-meryl meryl print reads.meryl

Helper commands are exposed through command mode:

taf-meryl meryl-lookup
taf-meryl meryl-import
taf-meryl meryl-analyze
taf-meryl meryl-simple

position-lookup is included because it is part of the official binary release, but it expects valid positional inputs and is not useful as a no-argument help probe.

Data Model

Modern Meryl databases are directories, not the old .mcdat and .mcidx files from Canu 1.8-era Meryl. Keep the whole .meryl directory together when moving or mounting results.

Typical count output:

taf-meryl meryl k=21 memory=64 count reads.fastq.gz output reads.meryl

The output directory is overwritten only as allowed by upstream Meryl. Choose a fresh output path for repeatable runs.

Platform

This release is native linux/amd64 only. The upstream Meryl 1.4.1 release ships a Linux-amd64 binary asset and Darwin-amd64 asset, but no Linux-arm64 binary asset. Source/native arm64 builds are not claimed here because the current upstream source path still depends on x86 SSE code in parts of the alignment utility code.

For Docker and Podman, the TAFFISH wrapper declares --platform linux/amd64 in src/main.taf, so arm64 hosts can run it through amd64 emulation when the container backend supports that. This is emulated execution, not native linux/arm64 support. Apptainer behavior on non-amd64 hosts depends on the site runtime and is not declared as supported by this app.

Smoke Coverage

The app smoke tests check:

• packaged version marker and meryl --version;
• main help and helper command usage output;
• presence of all official binary commands;
• runtime dynamic dependency on libgomp;
• compression utilities gzip, bzip2, and xz;
• a tiny real meryl count, followed by histogram, statistics, and print.

These checks verify packaging and a minimal functional path. They do not replace large-scale biological validation, memory sizing tests, or project-specific quality-control interpretation.

Boundaries

This app packages Meryl itself. It does not include Merqury, GenomeScope, assembly plotting/report workflows, or large example datasets. Use the separate taf-merqury app for the Merqury assembly-evaluation workflow.

License Boundary

The TAFFISH app packaging files are licensed under Apache-2.0. The packaged upstream Meryl software is covered by: Public Domain. Bundled third-party components, datasets, models, and external resources keep their own license terms.

Upstream

• Upstream repository: https://github.com/marbl/meryl
• Release: https://github.com/marbl/meryl/releases/tag/v1.4.1
• Upstream license: public domain notice in upstream README.licenses, with additional notices as indicated by upstream
• Citation: Rhie et al. 2020, Genome Biology 21, 245
• DOI: https://doi.org/10.1186/s13059-020-02134-9
• PMID: 32928274