bps-fbi-sp-ecoli 0.0.6

Species specific scripts for ecoli

bps_fbi_sp_ecoli

Installation

Note that this program requires KMA, which is not available on pip. you would need to install it via conda or github.

Installation with pip

conda create /.venv python=3.11
pip install bps_fbi_sp_ecoli
conda install bioconda::kma

Installation with conda

conda create /.venv python=3.11
conda install kalilamali::bps_fbi_sp_ecoli
pip install requirements.txt

How to use

Determines the serotype and virulence in ecoli through kmer alignment

! FBI_run_bifrostecolipostkma -h

#! FBI_run_bifrostecolipostkma --input input/231116_CUSTOM_SSIFBI_ECOLI --sample_sheet sample_sheet.xlsx --output output --db_path input/db/ecoligenes --execute

! FBI_run_qcecolisummary -h

#! FBI_run_qcecolisummary --input output/231116_CUSTOM_SSIFBI_ECOLI --output output --execute