ArticleMicrobial genomics2024
A practical guide and Galaxy workflow to avoid inter-plasmidic repeat collapse and false gene loss in Unicycler's hybrid assemblies.
Article in Microbial genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 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
4 citing papers in PubMed, 7 citations in OpenAlex.
- Extensively Drug-Resistant ST16Infection and drug resistance · 2026Article
- Mitochondrial genome complexity in Erodium stephanianum (Geraniaceae): nanopore sequencing reveals chloroplast gene transfer and DNA rearrangements.Frontiers in genetics · 2025Article
- Contributions of Long-Read Sequencing for the Detection of Antimicrobial Resistance.Pathogens (Basel, Switzerland) · 2024Article
- Whole-genome sequence ofMicrobiology resource announcements · 2024Article
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 at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Generating complete, high-quality genome assemblies is key for any downstream analysis, such as comparative genomics. For bacterial genome assembly, various algorithms and fully automated pipelines exist, which are free-of-charge and easily accessible. However, these assembly tools often cannot unambiguously resolve a bacterial genome, for example due to the presence of sequence repeat structures on the chromosome or on plasmids. Then, a more sophisticated approach and/or manual curation is needed. Such modifications can be challenging, especially for non-bioinformaticians, because they are generally not considered as a straightforward process. In this study, we propose a standardized approach for manual genome completion focusing on the popular hybrid assembly pipeline Unicycler. The provided Galaxy workflow addresses two weaknesses in Unicycler's hybrid assemblies: (i) collapse of inter-plasmidic repeats and (ii) false loss of single-copy sequences. To demonstrate and validate how to detect and resolve these assembly errors, we use two genomes from the
Indexed as
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.