We assume your current directory points to this directory (d6_ecoli_r104).
Run RawHash2 to map the raw nanopore signals to the corresponding reference genome. This will create the rawhash2 directory including a PAF file that stores the mapping output from RawHash2.
The following command will use 32 threads. you can change the maximum threads to use by providing a different value than 32 below.
bash run_rawhash2.sh 32UNCALLED currently does not support R10 reads .
Sigmap currently does not support R10 reads.
Run minimap2 to map the basecalled sequences to the corresponding reference genome. This will create the true_mappings.paf file that includes the ground truth mapping output from minimap2.
The following command will use 32 threads. you can change the maximum threads to use by providing a different value than 32 below.
bash run_minimap2.sh 32Comparison is not possible. However, in order to generate the RawHash2 results with the existing scripts, we generate the symbolic links of UNCALLED an Sigmap results in the comparison directory.
After generating the PAF files by following each step above, run the following command. This will 1) generate the files to evaluate the mapping output of RawHash2 and 2) output the results (i.e., throughput, mean time per read, indexing time, mapping time, precision, recall, and F1 values).
cd comparison
bash 0_run.sh
#After running 0_run.sh, if you want to just summarize the results again without generating the evaluation files, you can alternatively run the following command:
# bash 2_output_results.sh
cd ..