oschwengers/asap repository overview

ASA³P is an automatic and highly scalable assembly, annotation and higher-level analyses pipeline for closely related bacterial isolates. It is developed as a command line tool creating standard bioinformatics file formats as well as sophisticated HTML5 documents. Its main purpose is the automatic processing of large scale NGS data, thus transforming raw reads into assembled and annotated genomes and finally getting as much information on every single bacterial genome as possible. Per-isolate analyses are finally complemented by first comparative insights. Hereby, the software incorporates many best-in-class open source bioinformatics tools and thus takes away the burden of ever repeating tasks from its users. Envisaged as an upfront 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 presenting all this by interactive modern HTML5 documents to the user. For more information please have a look at https://github.com/oschwengers/asap⁠

Schwengers et al. (2020). ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher level analysis of closely related bacterial isolates. PLOS Computational Biology 16(3): e1007134. https://doi.org/10.1371/journal.pcbi.1007134⁠

All necessary files are available via Zenodo (https://doi.org/10.5281/zenodo.3606299⁠):

• ASA³P directory tarball (software & databases) (necessary): asap.tar.gz (md5: a2dcb3465bcbace5930eb278e91bf395)
• configuration spreadsheet template (necessary): config.xls
• comprehensive manual: manual.pdf

Exemplary and benchmark datasets are available via a distinct Zenodo repository (https://doi.org/10.5281/zenodo.3606760⁠):

• 4 L. monocytogenes project: example-lmonocytogenes-4.tar.gz (md5: 3da5858e62a3c8a836dfa91e58a9983e)
• 32 L. monocytogenes project: example-lmonocytogenes-32.tar.gz (md5: 4e64aa96f24dff518dead76f150a936c)
• 8 E. coli project: example-ecoli-input.tar.gz (md5: 1da85ab18f9afae98cf176ef88c6c214)
• exemplary config spreadsheet: config-example.xls

Note: As the ASA³P tarball contains all necessary databases and 3rd party executables, it is rather huge (78 Gb zipped, 142 Gb unzipped) and thus, download times may be very long. To unzip the tarball a deflating tool supporting multithreadding might be beneficial, e.g. pigz on linux (sudo apt install pigz for Ubuntu).

Source code, manuals, configuration files are publicly accessible at GitHub: https://github.com/oschwengers/asap⁠

License ASA³P itself is published and distributed under GPL3 license. In contradiction, some of its dependencies bundled within the ASA³P directory (asap.tar.gz file) are published under different licenses, e.g. GPL2, BSD, MIT, LGPL, etc. A file (README.md) within the ASA³P directory contains a list of all dependencies and licenses.

Please notice that some bundled dependencies are published under a free-for-academic or free-for-non-commercial usage license model. To our best knowledge this is true for at least the following databases:

• CARD: free for academic usage
• PubMLST: proprietary but free to use