ArticleMicrobial genomics2024
How low can you go? Short-read polishing of Oxford Nanopore bacterial genome 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 95 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
95 citing papers in PubMed.
- Article
- Whole-Genome Sequencing Analysis of ST1, ST11, ST17, and ST37Microorganisms · 2026Article
- The Oxytetracycline ProducerInternational journal of molecular sciences · 2026Article
- Complete genome sequence ofMicrobiology resource announcements · 2026Article
- Genome-based predictions of metabolic preferences and substrate phenotypes in psychrotrophic bacteria from permafrost environments.Microbiology spectrum · 2026Article
- Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5.Bioinformatics (Oxford, England) · 2026Article
- Adaptive Laboratory Evolution of the Hydrocarbonoclastic Marine Strain Rhodococcus ruber MSA14 to High Pyrene Concentrations.Current microbiology · 2026Article
- Deployable high-fidelity metagenome binning at scale with QuickBin.Communications biology · 2026Article
- Draft genome ofMicrobiology resource announcements · 2026Article
- Lineage-associated differences in adenine methylation patterns of mammalian-associatedMicrobiology spectrum · 2026Article
- Quantitative comparison of fungal genome assembly strategies using short and long reads from simulated and empirical sequencing data.Microbial genomics · 2026Article
- Insertion sequence elements associated with Staphylococcus epidermidis evolution in persistent orthopaedic device-related infections.BMC genomics · 2026Article
- Complete genome sequence ofMicrobiology resource announcements · 2026Article
- Complete genome sequences ofMicrobiology resource announcements · 2026Article
- Sequencing the genome ofMicrobiology resource announcements · 2026Article
- The pQBR mercury resistance plasmids: a model set of sympatric environmental mobile genetic elements.Microbial genomics · 2026Article
- Enhanced invasiveness promotes the dominance of a widely-distributed carbapenem-resistant virulence-plasmid-carrying Klebsiella pneumoniae sublineage.Nature communications · 2026Article
- Genomic analysis identifies candidate SOS-associated and EPS/envelope-remodeling islands in a drinking-water Stenotrophomonas maltophilia complex isolate.Scientific reports · 2026Article
- Complete genome sequence ofMicrobiology resource announcements · 2026Article
- Complete genome sequence ofMicrobiology resource announcements · 2026Article
35 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
It is now possible to assemble near-perfect bacterial genomes using Oxford Nanopore Technologies (ONT) long reads, but short-read polishing is usually required for perfection. However, the effect of short-read depth on polishing performance is not well understood. Here, we introduce Pypolca (with default and careful parameters) and Polypolish v0.6.0 (with a new careful parameter). We then show that: (1) all polishers other than Pypolca-careful, Polypolish-default and Polypolish-careful commonly introduce false-positive errors at low read depth; (2) most of the benefit of short-read polishing occurs by 25× depth; (3) Polypolish-careful almost never introduces false-positive errors at any depth; and (4) Pypolca-careful is the single most effective polisher. Overall, we recommend the following polishing strategies: Polypolish-careful alone when depth is very low (<5×), Polypolish-careful and Pypolca-careful when depth is low (5-25×), and Polypolish-default and Pypolca-careful when depth is sufficient (>25×).
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.