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ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates

Bacterial whole-genome sequencing has become daily routine in many fields. Technical advances and dropping costs have resulted in a tremendous increase in available sequence data. However, the comprehensive in-depth analysis thereof remains an arduous and time-consuming task. Here, we introduce ASA³P, a fully automatic, locally executable and scalable assembly, annotation and analysis pipeline for bacterial genomes. The pipeline conducts necessary raw data processing steps as well as comprehensive genome characterizations, e.g. taxonomic classification, detection of AMR genes and virulence factors and much more. The workflow is implemented in a fully-automatic manner, scaling from tiny to very large cohorts via a portable Docker image or a highly-scalable cloud version. All results are presented via interactive HTML reports.

Background

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.

 

Results

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.

 

Citation

Schwengers, O., Hoek, A., Fritzenwanker, M., Falgenhauer, L., Hain, T., Chakraborty, T., & Goesmann, A.

ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates.

PLoS Computational Biology (2020), 16(3), e1007134. DOI: 10.1371/journal.pcbi.1007134