d2_ecoli_r94

Read Mapping - d2_ecoli_r94

We assume your current directory points to this directory (d2_ecoli_r94).

RawHash2

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 32

The following command will use the POD5 files (if you generated them):

bash run_rawhash2_pod5.sh 32

RawHash

Run RawHash to map the raw nanopore signals to the corresponding reference genome. This will create the rawhash directory including a PAF file that stores the mapping output from RawHash.

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_rawhash.sh 32

The following command will use the POD5 files (if you generated them):

bash run_rawhash_pod5.sh 32

UNCALLED

Run UNCALLED to map the raw nanopore signals to the corresponding reference genome. This will create the uncalled directory including a PAF file that stores the mapping output from UNCALLED.

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_uncalled.sh 32

Sigmap

Run Sigmap to map the raw nanopore signals to the corresponding reference genome. This will create the sigmap directory including a PAF file that stores the mapping output from Sigmap.

Important: Sigmap will require around 110GB of peak memory during this run.

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_sigmap.sh 32

Ground truth mapping (minimap2)

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 32

Comparing RawHash2 to RawHash, UNCALLED and Sigmap

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 each tool 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 ..

Profiling RawHash2

We have created a script to profile the main steps of RawHash2 (i.e., I/O, signal-to-event conversion, sketching, seeding, chaining, and the entire mapping). Before running the following script, RawHash2 needs to be compiled with the profiling mode. Please compile as follows:

# For profiling
make PROFILE=1

After compiling with the profiling mode and adding RawHash2 to your path, you can run the following script to generate the profilied runtimes. The profiling result will be directed to stderr.

bash profile_rawhash2.sh 1