Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111
Usage
| Version | module name |
|---|
| 1.2. | 13 | cactus/1.2. | 13 |
| 1.23.30 | cactus/1.2.3 |
Command line option to run cactus
| Code Block |
|---|
|
cactus <jobStorePath> <seqFile> <outputHal> --binariesMode singularity --maxCores |
...
| Code Block |
|---|
| language | bash |
|---|
| title | Example: /share/Apps/examples/cactus |
|---|
| collapse | true |
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|
#!/bin/bash
#SBATCH -p debug
#SBATCH -n 16
#SBATCH -N 1
#SBATCH -t 90
#SBATCH -J cactus
module load cactus/1.3.0
cd ${SLURM_SUBMIT_DIR}
cactus jobStore examples/evolverMammals.txt examples/evolverMammals.hal --root mr --binariesMode singularity --maxCores ${SLURM_NTASKS}
|
More Information: https://github.com/ComparativeGenomicsToolkit/cactus