Beschrijving
Pacini-typing is a user-friendly command-line application for the detection of DNA sequences and Single Nucleotide Polymorphisms (SNPs) in both FASTA and FASTQ genome files. It was primarily developed for genotyping Yersinia pestis and Vibrio cholerae, but is designed to be flexible and applicable to other bacterial species.
The application is configured via a YAML-based configuration file and supports three search modes: gene detection, SNP detection, or both. It uses BLAST and KMA as underlying alignment tools and produces CSV output reports with detailed hit information including percentage identity, coverage, and e-values.
Pacini-typing is available via Bioconda and can be installed with conda install bioconda::pacini_typing.
Gendetectie in FASTA- en FASTQ-genoombestanden via BLASTSNP-detectie met KMA en PointFinderYAML-configuratie voor flexibele genotyperingsschema'sCSV-uitvoer met identiteit, dekking en e-waarden per trefferOptionele FASTA-uitvoer van gevonden sequentiesBeschikbaar via Bioconda voor eenvoudige installatie