Main tool: el_gato
Code repository: https://github.com/appliedbinf/el_gato
Additional tools:
- minimap2: 2.24-r1122
- samtools: 1.13
- ncbi-blast+: 2.12.0+
- isPCR: v33x2
Basic information on how to use this tool:
- executable: el_gato.py
- help: -h
- version: -v
- description: Epidemiology of Legionella : Genome-bAsed Typing
Additional information:
Container contains necessary database of Legionella sequence types
Full documentation: https://github.com/appliedbinf/el_gato
# Paired-end:
el_gato.py --read1 read1.fastq.gz --read2 read2.fastq.gz --out output_folder/
# Assembly:
el_gato.py --assembly assembly_file.fna --out output_folder/