NOMADIC is a collection of python scripts for analysing long read data generated from Plasmodium falciparum malaria. The scripts are assembled into a pipeline that can be run locally or on an Oracle Grid Engine cluster.
At present, the focus is nanopore data generated for a panel of target amplicons.
First, we build a virtual environment including all dependencies using conda:
conda update conda
conda env create
conda activate nomadic2
Next, we locally install the python package nomadic2 into this virtual environment using pip:
pip install .
First, output data from minknow and a metadata file must be arranged into the experiments directory. See experiments/0000-00-00_example for an example. Then, the full pipeline can be run by invoking:
nomadic runall -e experiments/0000-00-00_example -c configs/default.ini
Where 0000-00-00_example would be replaced with your experiment of interest. The configuration file contains information about basecalling settings, target amplicons and mutations. It can be changed to suit your assay.
A full list of commands can be found by typing nomadic:
Usage: nomadic [OPTIONS] COMMAND [ARGS]...
NOMADIC: A pipeline for analysis of malaria long-read data
Options:
--help Show this message and exit.
Commands:
bmrc Build BMRC pipeline submission.
map Map to P.f. reference.
qcbams QC analysis of .bam files.
remap Map unmapped reads to H.s.
runall Run complete pipeline.
targets Analyse amplicon targets.