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Pipeline for telomere-to-telomere QC of genome assemblies.

Performs:

• Basic assembly length statistics
• Telomere motif scanning at contig ends
• Identification of “primary” contigs (covering ~98% assembly length)
• N-run (gap) detection and per-contig summary
• Clustering of gaps into biological gap groups
• Genome-wide and per-chromosome gap-distribution plots

Required input: a genome assembly FASTA file.

Run with:

qsub -v FASTA=assembly.fa,PREFIX=my_sample t2t_qc.pbs

Optional parameters:

TELOMERE_MOTIF     (default: TTTAGGG)
TELOMERE_WINDOW    (default: 200000)
THREADS            (default: 8)
GAP_CLUSTER_DIST   (default: 1000000)
CONDA_ENV          (path to Conda environment)

Create a conda environment:

conda create -n t2tqc samtools gnuplot python minimap2 -c bioconda -c conda-forge

Run using an activated environment:

conda activate t2tqc
qsub -v FASTA=assembly.fa,PREFIX=my_sample t2t_qc.pbs

Or pass the environment directly:

qsub -v FASTA=assembly.fa,PREFIX=my_sample,CONDA_ENV=/path/to/env t2t_qc.pbs

The following outputs are generated (PREFIX = chosen prefix):

• PREFIX.lengths.tsv

• PREFIX.contigs_telomeres.tsv

• PREFIX.contigs_primary.tsv
• primary_chroms.tsv

• PREFIX.gaps.stats.tsv
• PREFIX.gaps.bed

• PREFIX.gaps.clustered.bed
• PREFIX.gaps.clusters.stats.tsv

• PREFIX.gaps_per_chr.N_clusters.png
• PREFIX.gaps_genome.N_clusters.png

t2t-qc/
  t2t_qc.pbs
  README.md
  scripts/
    00_basic_stats.sh
    01_telomere_scan.sh
    02_primary_contigs.sh
    03_gap_stats.sh
    04_cluster_gaps.sh
    05_plot_per_chr.sh
    06_plot_genome.sh

If you use t2t-qc in your research, please cite:

Boutsika, A. (2025). t2t-qc: Pipeline for telomere-to-telomere genome assembly QC  
(Version 1.0.0) [Computer software]. Zenodo.  
https://doi.org/10.5281/zenodo.17855666

BibTeX:

@software{boutsika_2025_t2tqc,
  author       = {Boutsika, Anastasia},
  title        = {t2t-qc: Pipeline for telomere-to-telomere genome assembly QC},
  month        = jan,
  year         = 2025,
  publisher    = {Zenodo},
  version      = {1.0.0},
  doi          = {10.5281/zenodo.17855666},
  url          = {https://doi.org/10.5281/zenodo.17855666}
}