AmpliSAT
Dear Users – the AmpliSAT web server is no longer maintained!
However, many AmpliSAT tools – including AmpliSAS, AmpliCOMBINE, AmpliCOMPARE, AmpliTCR, and AmpliCDR3 – remain available for use through local installation as Linux-based command-line tools.
We suggest installing AmpliSAT via CONDA. Installation instructions can be found here:
https://github.com/TomekGa/amplisat#server-installation
For merging reads, we currently recommend using external software such as PEAR:
https://cme.h-its.org/exelixis/web/software/pear/doc.html
Files for download:
- Detailed instructions for command-line usage are available in this PDF (with more advanced example)
- Updated AmpliSAT manual – with legacy information about web server and instructions for command-line usage (simple example)
- Example files to run analysis are available in the conda repository here. Merged reads of the example fq files are available here
- For users familiar with the former web server settings – an Excel file with a “translation” of parameters from the previous web server version to their corresponding command-line usage
When using local installations please cite:
Sebastian, A., Migalska, M., Gaczorek, T. (2024). AmpliSAS and AmpliHLA: Web Server and Local Tools for MHC Typing of Non-model Species and Human Using NGS Data. In: Boegel, S. (eds) HLA Typing. Methods in Molecular Biology, vol 2809. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3874-3_3
Alongside the original publication:
Sebastian A, Herdegen M, Migalska M, Radwan J. AMPLISAS: a web server for multilocus genotyping using next-generation amplicon sequencing data. Mol Ecol Resour. 2016;16(2):498-510. doi:10.1111/1755-0998.12453
For assistance and questions please contact: magda.migalska (at) uj.edu.pl