ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2020
Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 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
36 citing papers in PubMed.
- Genome-wide analysis reveals structured ecological and functional divergence within Geobacillus stearothermophilus.Scientific reports · 2026Article
- Isolation and genetic analysis of anBiochemistry and biophysics reports · 2026Article
- Draft genome sequences ofMicrobiology resource announcements · 2026Article
- Population structure reveals clade- and region-specific dissemination of macrolide-resistantFrontiers in cellular and infection microbiology · 2026Article
- Genomics of Shiga toxin-producing Escherichia coli from asymptomatic carriers in Japan highlights risk-adaptive control.Communications biology · 2025Article
- Pseudomonas fragi or not? Beyond MALDI-TOF in the frontier of Pseudomonas diversity.Medical microbiology and immunology · 2025Article
- Furfurilactobacillus entadae sp. nov., Isolated from Bark of Entada phaseoloides.Current microbiology · 2025Article
- Draft genome sequences ofMicrobiology resource announcements · 2025Article
- Genomic features of three major diarrhoeagenicMicrobial genomics · 2025Article
- GAS-J, a User-Friendly Browser Application for Genome Assembly, emm-Typing, MLST Typing, and Virulence Factor Gene Detection of Streptococcus pyogenes.Microbiology and immunology · 2025Article
- Risk of multidrug resistance in Escherichia coli associated with routine antimicrobial prophylaxis on pig farms.npj antimicrobials and resistance · 2025Article
- Comprehensive serotyping of Mannheimia haemolytica by a PCR system using the diversity of capsule biosynthesis genes.Scientific reports · 2025Article
- Whole-genome-based characterization ofMicrobial genomics · 2025Article
- Article
- Genome Analysis of Japanese Yersinia pseudotuberculosis Strains Isolated From Kawasaki Disease Patients and Other Sources and Their Phylogenetic Positions in the Global Y. pseudotuberculosis Population.Microbiology and immunology · 2025Article
- Proliferation of a bloom-forming phytoplankton via uptake of polyphosphate-accumulating bacteria under phosphate-limiting conditions.ISME communications · 2025Article
- Mobile genetic element-driven genomic changes in a community-associated methicillin-resistantMicrobial genomics · 2024Article
- Complete genome sequences of 11Microbiology resource announcements · 2024Article
- Draft Genome Sequence of Acinetobacter calcoaceticus TUS-SO1, a Bacterium Capable of Degrading 2-Phenoxyacetophenone.Microbiology resource announcements · 2023Article
- Draft Genome Sequences of Endophytic Pseudomonas Strains, Isolated from the Interior ofMicrobiology resource announcements · 2023Article
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
No grant is acknowledged in the PubMed record.
Abstract
De novo assembly of short DNA reads remains an essential technology, especially for large-scale projects and high-resolution variant analyses in epidemiology. However, the existing tools often lack sufficient accuracy required to compare closely related strains. To facilitate such studies on bacterial genomes, we developed Platanus_B, a de novo assembler that employs iterations of multiple error-removal algorithms. The benchmarks demonstrated the superior accuracy and high contiguity of Platanus_B, in addition to its ability to enhance the hybrid assembly of both short and nanopore long reads. Although the hybrid strategies for short and long reads were effective in achieving near full-length genomes, we found that short-read-only assemblies generated with Platanus_B were sufficient to obtain ≥90% of exact coding sequences in most cases. In addition, while nanopore long-read-only assemblies lacked fine-scale accuracies, inclusion of short reads was effective in improving the accuracies. Platanus_B can, therefore, be used for comprehensive genomic surveillances of bacterial pathogens and high-resolution phylogenomic analyses of a wide range of bacteria.
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.