ASA³P is an automatic and highly scalable assembly, annotation and higher-level analyses pipeline for closely related bacterial isolates. https://github.com/oschwengers/asap ASA³P is a fully automatic, locally executable and scalable assembly, annotation and higher-level analysis pipeline creating results in standard bioinformatics file formats as well as sophisticated HTML5 documents. Its main purpose is the automatic processing of NGS WGS data of multiple closely related isolates, thus transforming raw reads into assembled and annotated genomes and finally gathering as much information on every single bacterial genome as possible. Per-isolate analyses are complemented by comparative insights. Therefore, the pipeline incorporates many best-in-class open source bioinformatics tools and thus minimizes the burden of ever-repeating tasks. Envisaged as a preprocessing tool it provides comprehensive insights as well as a general overview and comparison of analysed genomes along with all necessary result files for subsequent deeper analyses. All results are presented via modern HTML5 documents comprising interactive visualizations. Schwengers et al, 2020 PLOS Comp Bio DOI:10.1371/journal.pcbi.1007134

{"references": ["Schwengers et al. (2019). ASA\u00b3P: An automatic and scalable pipeline for the assembly, annotation and higher level analysis of closely related bacterial isolates. bioRxiv 654319; doi: https://doi.org/10.1101/654319"]}