A snakmake pipeline for comparing various safe paths with flowtigs in a De Bruijn graph of DNA reads in metagenomes. The pipeline also does all the pre-processing and the post-processing, and compares the results with structural contigs, extended contigs and unitigs.
The input dataset should be a folder located in the folder data/meta/ from the root of this project. The input folder should contain all the genome reads as fasta files with the ending ".fasta" or ".fna". The folder can contain other files as long as they don't have these endings.
The output of this pipeline is the LaTeX file data/reports/output/meta_<name-of-the-input-folder>_k31ma1t28nm1/<report-name>/report.tex. The figures of the latex file can be found in the folder data/reports/hashdir.
The following has to be done once before running the pipeline.
- Install conda.
- Create the conda environment with the command
conda env create -f environment.ymlin the root of this project.
To run the pipeline:
- Activate the environment with the command
conda activate snakemake-flowtigs. - Execute the pipeline with the command
snakemake -j 1 "<path-to-this-project>/data/reports/output/meta_<name-of-the-input-folder>_k31ma1t28nm1/<report-name>/report.tex".
The pipeline parameters can be changed by modifying the k31ma1t28nm1 part of the running command. This will also change the name of the output file accordingly. The four parameters are represented by characters, followed by an integer indicating their value:
- k: size of the k-mers used in the De Bruijn graph.
- ma: minimum adundance.
- t: number of threads used.
- nm: binary value representing whether or not to append the unitigs to the results of the other safe-walk-algorithms. Use 1 to append unitigs, and 0 to not append them.