Get it directly
The quarTeT toolkit is freely available under the MIT license, and is provided without warranty.
For details on usage, please refer to the Tutorial section. If you have any questions, feel free to contact us.
Alternative installation methods
In addition to the standalone tarball, quarTeT is also available via Conda, Docker, and Singularity:
Conda
conda install --channel conda-forge --channel bioconda quartet-bio
mamba install --channel conda-forge --channel bioconda quartet-bio
mamba install --channel conda-forge --channel bioconda quartet-bio
Docker
docker pull quay.io/biocontainers/quartet-bio:<version>--<hash>
Singularity
singularity pull docker://quay.io/biocontainers/quartet-bio:<version>--<hash>
Note: Replace <version>--<hash> with the actual version tag (e.g., 1.3.1--abc123). Check the Quay.io repository for available tags.
Dependencies
| Dependency | Recommended version | External links |
|---|---|---|
| Python3 | >3.6 | https://www.python.org/ |
| Minimap2 | ≥2.24 | https://github.com/lh3/minimap2 |
| Unimap | ≥0.1 | https://github.com/lh3/unimap |
| MUMmer4 | ≥4.0.0rc1 | https://github.com/mummer4/mummer |
| trf | ≥4.09 | https://github.com/Benson-Genomics-Lab/TRF |
| CD-hit | ≥4.8.1 | https://github.com/weizhongli/cdhit |
| BLAST+ | ≥2.11.0 | https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ |
| tidk | ≥0.2.31 | https://github.com/tolkit/telomeric-identifier |
| gnuplot | ≥5.4 | https://github.com/gnuplot/gnuplot |
| R | ≥3.5.0 | https://www.R-project.org/ |
| RIdeogram | ≥0.2.2 | https://CRAN.R-project.org/package=RIdeogram |
| ggplot2 | ≥3.4.4 | https://cran.r-project.org/web/packages/ggplot2 |
Test Data
| File | Description |
|---|---|
| contig.fasta.gz | Phased contig level assembly. Used in AssemblyMapper. |
| reference_genome.fasta.gz | Close related reference genome sequence. Used in AssemblyMapper. |
| draft_genome.fasta.gz | Draft chromosome level assembly generated by AssemblyMapper. Used in GapFiller. |
| gap_closer_sequence.fasta.gz | Long sequence from other sequencing platform. Used in GapFiller. |
| final_genome.fasta.gz | Final genome generated by GapFiller. Used in TeloExplorer and CentroMiner. |
| TE_annotation.gff3.gz | TE annotation of the final genome above. Optionally used in CentroMiner. |