ArticlePLoS computational biology2020
ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- PROBEAT: PRObiotic Bacterial gEnome Analysis Toolkit.Current issues in molecular biology · 2026Article
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- Phenotypic and genome-based characterization ofFrontiers in microbiology · 2026Article
- Impact of sequencing read quality on whole-genome sequencing outcomes for foodborne pathogens using a BacWORK standardized analysis workflow.Bioinformatics advances · 2026Article
- Enteroflow: Automated Pipeline for In Silico Characterization ofInternational journal of molecular sciences · 2025Article
- Genome-based development and clinical evaluation of a customized LAMP panel to rapidly detect, quantify, and determine antibiotic sensitivity of Escherichia coli in native urine samples from urological patients.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2025Article
- The Detection of Extensively Drug-ResistantMicroorganisms · 2025Article
- Solu: a cloud platform for real-time genomic pathogen surveillance.BMC bioinformatics · 2025Article
- Article
- BacExplorer: an integrated platform forBioinformatics advances · 2025Article
- zDB: bacterial comparative genomics made easy.mSystems · 2024Article
- AMRomics: a scalable workflow to analyze large microbial genome collections.BMC genomics · 2024Article
- BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets.Nucleic acids research · 2024Article
- AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance.BMC bioinformatics · 2024Article
- Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies.Microbial genomics · 2024Article
- Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies.bioRxiv : the preprint server for biology · 2024Article
- Whole genome sequencing data ofData in brief · 2024Article
- Draft genome sequences ofMicrobiology resource announcements · 2024Article
- Predominant transmission of KPC-2 carbapenemase in Germany by a unique IncN plasmid variant harboring a novel non-transposable element (NTEMicrobiology spectrum · 2024Article
- Comparative genomic characterization ofFrontiers in microbiology · 2024Article
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7 authors.
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Abstract
Whole genome sequencing of bacteria has become daily routine in many fields. Advances in DNA sequencing technologies and continuously dropping costs have resulted in a tremendous increase in the amounts of available sequence data. However, comprehensive in-depth analysis of the resulting data remains an arduous and time-consuming task. In order to keep pace with these promising but challenging developments and to transform raw data into valuable information, standardized analyses and scalable software tools are needed. Here, we introduce ASA3P, a fully automatic, locally executable and scalable assembly, annotation and analysis pipeline for bacterial genomes. The pipeline automatically executes necessary data processing steps, i.e. quality clipping and assembly of raw sequencing reads, scaffolding of contigs and annotation of the resulting genome sequences. Furthermore, ASA3P conducts comprehensive genome characterizations and analyses, e.g. taxonomic classification, detection of antibiotic resistance genes and identification of virulence factors. All results are presented via an HTML5 user interface providing aggregated information, interactive visualizations and access to intermediate results in standard bioinformatics file formats. We distribute ASA3P in two versions: a locally executable Docker container for small-to-medium-scale projects and an OpenStack based cloud computing version able to automatically create and manage self-scaling compute clusters. Thus, automatic and standardized analysis of hundreds of bacterial genomes becomes feasible within hours. The software and further information is available at: asap.computational.bio.
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