Campylobacter Gnomic Species Typer. A python script for accurate assignment of ANI genomic species to Campylobacter genomes.
conda install -c bioconda campygstyper
git clone https://github.com/LanLab/campygstyper.git
cd campygstyper
python setup.py install
Note following dependencies must be installed
- fastANI
campygstyper [-h] -i QUERYFOLDER -o OUTPUTFILE [-t THREADS]
-h, --help show this help message and exit
-i,--query QUERY folder containing all input genomes (genomes must have *.fasta suffix)
-o,--output tabular output file with classifications for each genome in query folder
-t, --thread number of threads to run fastANI with (default: 4)
A tab delimited file with the following columns:
- Query Genome : genome name extracted from file name
- Highest ANI Value : The highest ANI value of the query when compared to all centroid genomes
- Matching centroid genome : The accession of the highest matching centroid genome
- ANI cluster number : The cluster number that the centroid genome represents
- Campylobacter Genomic Species : The genomic species name assigned to the matching ANI cluster
- Possible Novel genomic species : Whether or not this genome does not match any centroid genome at 94.2% ANI. If True no centroid genomes match indicating that the genome could represent a new species. If True, highest match for other columns is still included but is not reliable.