We assume your current directory points to this directory (read_mapping)
Each directory includes the scripts to run RawHash, UNCALLED, Sigmap, and minimap2 for the corresponding dataset where the dataset name is specified in the directory name.
After running minimap2, each directory should include true_mappings.paf that can be used as the ground truth mapping information for the corresponding dataset.
After running RawHash, UNCALLED, and Sigmap, each directory should include subdirectories called rawhash, uncalled, and sigmap, which include the corresponding mapping output of each tool in PAF format.
Each directory includes a subdirectory called comparison where there are three scripts: 0_run.sh, 1_generate_results.sh, and 2_output_results.sh. These scripts use the output generated by each tool for a certain dataset to compare them each other. In each directory, we provide the README files that show how to use these scripts.
Please read the README file to run and compare the tools for this dataset.
To start mapping each tool, enter d1_sars-cov-2_r94
cd ./d1_sars-cov-2_r94Please read the README file to run and compare the tools for this dataset.
We provide the scripts for running RawHash with POD5 for this dataset
To start mapping each tool, enter d2_ecoli_r94
cd ./d2_ecoli_r94Please read the README file to run and compare the tools for this dataset.
To start mapping each tool, enter d3_yeast_r94
We provide the scripts for running RawHash with POD5 for this dataset
cd ./d3_yeast_r94Please read the README file to run and compare the tools for this dataset.
To start mapping each tool, enter d4_green_algae_r94
cd ./d4_green_algae_r94Please read the README file to run and compare the tools for this dataset.
To start mapping each tool, enter d5_human_na12878_r94
cd ./d5_human_na12878_r94This is the R10 dataset we use for experimental purposes
Please read the README file to run and compare the tools for this dataset.
To start mapping RawHash, enter d6_ecoli_r104
cd ./d6_ecoli_r104