elgato

el_gato

About : |

Epidemiology of Legionella : Genome-bAsed Typing:

El_gato is a bioinformatics tool that utilizes either a genome assembly (.fasta) or Illumina paired-end reads (.fastq) to replicate Legionella pneumophila Sequence Based Typing (SBT). From the input, 7 loci (flaA, pilE, asd, mip, mompS, proA, neuA/neuAh) are identified and compared to a database of sequence types. The sequence type provided for each input sample is based on the unique combination of the allelic identities of the 7 target loci.

Documentation : https://github.com/appliedbinf/el_gato

Citation :

Directory tree :

elgato/
├── elgato_summary.tsv
└── sample
    └── possible_mlsts.txt

Example file for an individual sample (possible_mlsts.txt)

Sample	ST	flaA	pilE	asd	mip	mompS	proA	neuA_neuAH
legionella_GCA_001753085.1	36	3	4	1	1	14	9	1

Example file for a run (elgato_summary.tsv)

Sample	ST	flaA	pilE	asd	mip	mompS	proA	neuA_neuAH
legionella_GCA_001753085.1	36	3	4	1	1	14	9	1