API Overview¶
- Version:
0.6.5
- Date:
Nov 20, 2023
Here we include and API documentation for BacterialTyper in order to provide third parties to use the
functionality of BacterialTyper application
This pipeline is composed of multiple modules and scripts that are separated in a main script:
BacterialTyper.py
This main script integrates and connects all available modules and analysis arranged in several directories:
BacterialTyper/modulesBacterialTyper/scriptsBacterialTyper/dataBacterialTyper/other_toolsBacterialTyper/config
Additionally, we include a third-party software named IslandPath-DIMOB. See additional details in section: IslandPath-DIMOB forked version.
third_party/IslandPath-DIMOB
Contents¶
- BacterialTyper
- Modules
- Scripts
- annotation
- ariba_caller
- bacteriophage
- blast_parser
- BUSCO_caller
- card_trick_caller
- database_generator
- database_user
- edirect_caller
- fastqc_caller
- functions
- genomic_island
- get_descendant
- min_hash_caller
- MLSTar
- multiQC_report
- sampleParser
- spades_assembler
- species_identification_KMA
- trimmomatic_call
- variant_calling
- virulence_resistance
- Config
- other_tools
- data
- Third Party Software