ArticleBioinformatics (Oxford, England)2025
Autocycler: long-read consensus assembly for bacterial genomes.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 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
78 citing papers in PubMed.
- Genomic global epidemiology and evolution ofMicrobial genomics · 2026Article
- Multiple Introductions and Cross-Sector Transmission of Salmonella enterica Serovar Infantis Carrying blaEmerging infectious diseases · 2026Article
- Structural and genetic dissection of RNA-guided gene repression by TnpB-derived transcription factors.bioRxiv : the preprint server for biology · 2026Article
- Whole-Genome Sequencing Analysis of ST1, ST11, ST17, and ST37Microorganisms · 2026Article
- Complete genome sequences of eight potential biocontrol microorganisms isolated from Washington apple orchards.Microbiology resource announcements · 2026Article
- Complete genome sequence ofMicrobiology resource announcements · 2026Article
- Complete genome sequence ofMicrobiology resource announcements · 2026Article
- Comparative Genomic Analysis of Clonal Variants of aMicroorganisms · 2026Article
- Adaptive Laboratory Evolution of the Hydrocarbonoclastic Marine Strain Rhodococcus ruber MSA14 to High Pyrene Concentrations.Current microbiology · 2026Article
- Genome sequences of 71 ecologically and geographically diverseMicrobiology resource announcements · 2026Article
- Draft genome ofMicrobiology resource announcements · 2026Article
- Complete genome sequence of multidrug-resistantMicrobiology resource announcements · 2026Article
- High-quality genome assembly and annotation of inactivated animal vaccine bacteria strains in South Korea.BMC genomic data · 2026Article
- Development andMicrobiology spectrum · 2026Article
- Human wastewater contamination drives the emergence of multidrug-resistant bacteria in the Galápagos marine ecosystem.Nature communications · 2026Article
- Genetic Background Modulates Zoliflodacin and Gepotidacin Cross-Resistance and Fitness in Neisseria gonorrhoeae.The Journal of infectious diseases · 2026Article
- Genomic diversity ofMicrobial genomics · 2026Article
- Competition constrains parasite adaptation to thermal heterogeneity.Evolution letters · 2026Article
- Complete genome sequence ofMicrobiology resource announcements · 2026Article
- Complete genome sequences ofMicrobiology resource announcements · 2026Article
18 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
3 authors.
Funding
Abstract
motivationLong-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using Trycycler can improve accuracy, but its lack of automation limits scalability. There is a need for an automated method to generate high-quality consensus bacterial genome assemblies from long-read data.
resultsWe present Autocycler, a command-line tool for generating accurate bacterial genome assemblies by combining multiple alternative long-read assemblies of the same genome. Without requiring user input, Autocycler builds a compacted De Bruijn graph from the input assemblies, clusters and filters contigs, trims overlaps, and resolves consensus sequences by selecting the most common variant at each locus. It also supports manual curation when desired, allowing users to refine assemblies in challenging or important cases. In our evaluation using Oxford Nanopore Technologies reads from five bacterial isolates, Autocycler outperformed individual assemblers, automated pipelines, and other consensus tools, producing assemblies with lower error rates and improved structural accuracy. AVAILABILITY AND IMPLEMENTATION: Autocycler is implemented in Rust, open-source, and freely available at github.com/rrwick/Autocycler. It runs on Linux and macOS and is extensively documented.
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.