ArticleBioinformatics advances2025
Genome Evaluation Pipeline (GEP): a fully automated quality control tool for parallel evaluation of genome assemblies.
Article in Bioinformatics advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
3 citing papers in PubMed.
- Snail plots are badges of genome assembly quality.G3 (Bethesda, Md.) · 2026Article
- The genomic basis of independent marine transitions in turtles: convergent episodic adaptation and demographic shifts.Molecular biology and evolution · 2026Article
- Whole-genome sequencing and biosynthetic gene cluster analysis of Bacillus subtilis BAGL as a potent antifungal biocontrol agent against phytopathogenic fungi.International microbiology : the official journal of the Spanish Society for Microbiology · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Summary: The ability to generate high-quality genome assemblies is paramount for understanding global biodiversity. To streamline the quality control of the vast amount of assemblies currently being generated, we developed the Genome Evaluation Pipeline (GEP). Our Snakemake-based command-line tool is composed of two modes and was designed taking into consideration the recommendations of different international projects to standardize genome evaluation across the Tree of Life. With the Build Mode, GEP generates k-mer databases from high-accuracy sequencing reads, incorporating optional quality control and pre-processing steps. The Evaluate Mode leverages these databases to assess genome assembly quality using standard, gene content, and k-mer based metrics. Key features include the assessment of genome characteristics such as size, heterozygosity, and ploidy without reference sequences, and the comparison of k-mer profiles to evaluate assembly completeness and correctness. GEP also supports flexible input options for k-mer databases and the integration of Hi-C data for visual inspection of the assembly structure. Finally, our tool produces comprehensive reports summarizing contiguity, completeness, and correctness metrics of genome assemblies, facilitating their comparison and selection for downstream studies. Availability and implementation: GEP is publicly available as a Git repository at https://git.imp.fu-berlin.de/begendiv/gep.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.