|
|
|
Campylobacter fetus subspecies determinationThis site assembles your paired end reads into genomes using Shovill and then analyzes them uses Cfvcatch. It places your isolate in a tree with reference isolates and finds resistance genes. Linda van der Graaf-van Bloois, Jaap Wagenaar, Aldert Zomer Introduction: Campylobacter fetus is a bacterial pathogen that causes disease in both animals and humans. It is composed of two subspecies, C. fetus subsp. fetus and C. fetus subsp. venerealis. Accurate identification of subspecies is important for the diagnosis and treatment of infections. Whole Genome Sequencing is the best method the distinguish the two subspecies from each other. In 2020, Abdel-Glil et al released Cfvcatch which automates most of the genome based classification. Here, we present a web-based bioinformatics tool that utilizes Cfvcatch, Mashtree and Abricate to analyze C. fetus genomes and distinguish between C. fetus subsp. fetus and C. fetus subsp. venerealis. It will also report resistance genes detected and place the isolate in a tree of reference isolates. Our tool provides a user-friendly interface to the aforementioned tools and allows for rapid and accurate identification of subspecies after uploading Illumina paired end reads or an assembled fasta file of your genome. Methods:
|
|
Instructions: Please fill in the isolate name (no spaces, only letters, numbers and dashes allowed), add your email address. Select the forward and reverse fastq.gz files from your computer OR selected the assembled genome as fasta file from your computer, and then press "Upload and run" |