ArticleBioinformatics (Oxford, England)2023
Plassembler: an automated bacterial plasmid assembly tool.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
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- From Wild to Farm: Gut Bacteriome Differences and Probiotic Potential of Pantoea Agglomerans in Two-Spotted Cricket (Gryllus Bimaculatus) Rearing.Probiotics and antimicrobial proteins · 2026Article
- Draft genome assemblies of doxycycline-resistant derivatives ofMicrobiology resource announcements · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
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- Pilosibacter rotomagensis sp. nov., a Butyrate-Producing Bacterium Isolated from Human Faeces.Current microbiology · 2026Article
- Cattle feces are a reservoir of diverse Acinetobacter species with potential to spread antibiotic resistance genes.Animal microbiome · 2026Article
- Genetic Characterization of Carbapenem-ResistantAntibiotics (Basel, Switzerland) · 2026Article
- Whole-genome sequences of 20Microbiology resource announcements · 2026Article
- Nanopore sequencing enables highly accurate genotyping and identification of resistance determinants in key nosocomial pathogens.Microbial genomics · 2026Article
- Carbapenemase-producing hypervirulentJournal of the Association of Medical Microbiology and Infectious Disease Canada = Journal officiel de l'Association pour la microbiologie medicale et l'infectiologie Canada · 2026Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryWith recent advances in sequencing technologies, it is now possible to obtain near-perfect complete bacterial chromosome assemblies cheaply and efficiently by combining a long-read-first assembly approach with short-read polishing. However, existing methods for assembling bacterial plasmids from long-read-first assemblies often misassemble or even miss bacterial plasmids entirely and accordingly require manual curation. Plassembler was developed to provide a tool that automatically assembles and outputs bacterial plasmids using a hybrid assembly approach. It achieves increased accuracy and computational efficiency compared to the existing gold standard tool Unicycler by removing chromosomal reads from the input read sets using a mapping approach. AVAILABILITY AND IMPLEMENTATION: Plassembler is implemented in Python and is installable as a bioconda package using 'conda install -c bioconda plassembler'. The source code is available on GitHub at https://github.com/gbouras13/plassembler. The full benchmarking pipeline can be found at https://github.com/gbouras13/plassembler_simulation_benchmarking, while the benchmarking input FASTQ and output files can be found at https://doi.org/10.5281/zenodo.7996690.
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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.