quartet

TAFFISH wrapper for quarTeT, a telomere-to-telomere toolkit for genome assembly finishing and chromosome feature analysis.

This app packages upstream quarTeT v1.3.1 as quartet 1.3.1-r1. The default TAFFISH command runs the upstream quartet console entry point. Command mode remains enabled, so the same container can also run bundled helper tools such as minimap2, nucmer, tidk, blastn, and Rscript.

Package metadata:

name: quartet
command: taf-quartet
version: 1.3.1-r1
kind: tool
image: ghcr.io/taffish/quartet:1.3.1-r1
upstream release: v1.3.1
upstream runtime version: version 1.3.1 in the quartet help banner

Quick Start

Show the TAFFISH package version:

taf-quartet --version

Show upstream quarTeT help. Because --help belongs to the TAFFISH wrapper, use -- or command mode to reach upstream help:

taf-quartet -- --help
taf-quartet quartet --help
taf-quartet quartet AssemblyMapper -h

Run the four upstream modules:

taf-quartet quartet AssemblyMapper -r reference.fa -q phased_contigs.fa -p sample -t 8 --noplot
taf-quartet quartet GapFiller -d draft.fa -g ultra_long_contigs.fa -p sample -t 8 --noplot
taf-quartet quartet TeloExplorer -i genome.fa -c plant -p sample
taf-quartet quartet CentroMiner -i genome.fa --TE te.gff3 --gene genes.gff3 -p sample -t 8

The module aliases are also upstream aliases:

taf-quartet quartet am ...
taf-quartet quartet gf ...
taf-quartet quartet te ...
taf-quartet quartet cm ...

Modules

AssemblyMapper / am   reference-guided ordering and orientation of phased contigs
GapFiller / gf        long-read or contig based gap filling
TeloExplorer / te     telomeric repeat discovery and terminal telomere calls
CentroMiner / cm      centromeric tandem-repeat candidate discovery

Common input formats are FASTA for genomes, contigs, and gap-closer sequences; GFF3 for optional TE and gene annotations in CentroMiner. The modules write prefix-based FASTA, AGP, tabular reports, and optional plot files in the current working directory.

Version 1.3.1 Notes

Upstream v1.3.1 changes gzip input behavior so gzipped FASTA and GFF inputs are read directly instead of being decompressed to sidecar files. This also fixes the upstream bug where symlinks pointing to gzipped files were not recognized as gzip input. The release also fixes CentroMiner handling of successful TRF runs across TRF return-code differences between v4.09 and v4.10.

The v1.3.0 layout changes are still included in this package:

quartet is the stable console entry point
AssemblyMapper includes --notelo
GapFiller join-mode handling is improved
runtime messages use Python logging

Container Contents

The image includes the upstream Python package plus the external tools called by quarTeT:

Python 3.12.13
minimap2 2.30
unimap 0.1
MUMmer4 4.0.1: nucmer, delta-filter, show-coords, mummerplot
TRF 4.10.0rc2
CD-HIT 4.8.1: cd-hit-est
BLAST+ 2.16.0: makeblastdb, blastn
tidk 0.2.65
gnuplot 6.0.4
R 4.5.3 with RIdeogram 0.2.2 and ggplot2 4.0.3
file, gzip, bash, GNU coreutils, and which

This keeps the upstream module set usable without asking users to assemble the hidden helper commands manually. Python 3.12 is used because upstream v1.3.x contains f-string syntax that fails under Python 3.10.

Notes And Boundaries

The image is native on both declared platforms:

linux/amd64
linux/arm64

The upstream CLI is preserved through taf-quartet quartet <module> .... Because this app keeps TAFFISH command mode enabled for helper commands, bare module names such as taf-quartet AssemblyMapper ... are interpreted as container executables and should not be used. taf-quartet minimap2 --version or taf-quartet Rscript -e 'library(ggplot2)' runs helper commands in the same container environment.

Plotting dependencies are bundled, including RIdeogram, ggplot2, gnuplot, and MUMmer plotting helpers. Upstream notes that conda-installed R may produce blank PNG files in some environments while SVG generation is correct; use --noplot for non-plotting runs or inspect generated SVG/PDF/PNG outputs for publication work.

quarTeT uses local temporary directories and prefix-based outputs. Run separate jobs in separate working directories or with distinct prefixes to avoid overwriting intermediate files.

Smoke Coverage

The package smoke checks are self-contained and offline. They verify:

quartet help banner and module help
Python package import and __version__
1.3.x help markers such as --notelo and --join-min-overlap
gzip symlink FASTA reading through the upstream utility layer
exact conda package versions for key dependencies
R package loading for RIdeogram and ggplot2
TeloExplorer on a tiny telomeric FASTA
AssemblyMapper on a tiny reference/contig pair
GapFiller on a tiny artificial gap and closer sequence
CentroMiner on a tiny tandem-repeat FASTA
MUMmer4 alignment helper path with nucmer, delta-filter, and show-coords

Smoke tests validate the container and small functional paths. They do not replace scientific validation on real assemblies, ultra-long reads, or centromere calls.

The TeloExplorer smoke uses a lower minimum-repeat threshold for its tiny synthetic FASTA; upstream default thresholds remain unchanged for normal runs.

Upstream

• Project: quarTeT
• Source: https://github.com/aaranyue/quarTeT
• Packaged release: https://github.com/aaranyue/quarTeT/releases/tag/v1.3.1
• Packaged source archive: https://github.com/aaranyue/quarTeT/archive/refs/tags/v1.3.1.tar.gz
• Source archive SHA256: 03a9d8b86eecc9de261b17d6297c681838759f0c16f31c44359be7247dec0e2b
• Upstream license: MIT
• Citation: Lin et al. 2023, Horticulture Research
• DOI: https://doi.org/10.1093/hr/uhad127
• PMID: https://pubmed.ncbi.nlm.nih.gov/37560017/

Maintainer Commands

taf check
docker build --platform linux/amd64 -t ghcr.io/taffish/quartet:1.3.1-r1 -f docker/Dockerfile .
docker build --platform linux/arm64 -t ghcr.io/taffish/quartet:1.3.1-r1-arm64-test -f docker/Dockerfile .
taf build
taf publish --build --release --dry-run

License

The TAFFISH packaging files are licensed under Apache-2.0. Upstream quarTeT v1.3.1 declares the MIT License.