TÍTULO : Análisis de genomas bacterianos, Klebsiella pneumoniae. Estrategia de secuenciación mixta: secuencias largas y cortas. Subtítulo: Genomic pathogenicity of OXA-48-producing Klebsiella pneumoniae clinical isolates.
AUTORA: Silvia García Cobos
This repository has phython scripts used during this TFM.
PYTHON SCRIPTS:
mlplasmid_RES_intersect.ipynb: This script allows the combination of results from mlplasmid software (contig prediction as plasmid or chromosome) and abricate software (presence/absence of genes of interest) results. In this case we are using abricate results based on ResFinder database: antibiotic resistance genes.
- input files: mlplasmid results in csv format and abricate results using ResFinder database (or another database for antibiotic resistance genes)
mlplasmid_vfkp_intersect.ipynb: This script allows the combination of results from mlplasmid software (contig prediction as plasmid or chromosome) and abricate software (presence/absence of genes of interest) results. In this case we are using abricate results based on a local virulence genes database.
- input files: mlplasmid results in csv format and abricate results using local database for virulence genes (or another database for virulence genes)
mlplasmid_plasREP_intersect.ipynb: This script allows the combination of results from mlplasmid software (contig prediction as plasmid or chromosome) and abricate software (presence/absence of genes of interest) results. In this case we are using abricate results based on PlasmidFinder database: plasmid replicon genes.
- input files: mlplasmid results in csv format and abricate results using PlasmidFinder database (plasmid replicon genes)
mlplasmid07_intersect_bySample.ipynb: This script allows the combination of results from mlplasmid software (contig prediction as plasmid or chromosome) and abricate software (presence/absence of genes of interest) results. For each database used, we can merge all genes predicted in plasmid contigs and in chromosomal contigs per isolate.
- input files: mlplasmid results grouped by isolate and plasmid/chromosome prediction (threshold posterior probability >0.7 or none) for each database of interest
CUSTOM DATABASE for Klebsiella pneumoniae virulence genes:
We created a customized local database - named vfkp - of the most relevant virulence genes for Klebsiella pneumoniae based on a scientific literature review and Klebsiella spp. curated public databases. It is included a formatted text and multifasta file to run it using abricate software.