reciprocal_smallest_distance
Link to section 'Introduction' of 'reciprocal_smallest_distance' Introduction
The reciprocal smallest distance (RSD) algorithm accurately infers orthologs between pairs of genomes by considering global sequence alignment and maximum likelihood evolutionary distance between sequences.
For more information, please check its home page on Github.
Link to section 'Versions' of 'reciprocal_smallest_distance' Versions
- 1.1.7
Link to section 'Commands' of 'reciprocal_smallest_distance' Commands
- rsd_search
- rsd_blast
- rsd_format
Link to section 'Module' of 'reciprocal_smallest_distance' Module
You can load the modules by:
module load biocontainers
module load reciprocal_smallest_distance
Link to section 'Example job' of 'reciprocal_smallest_distance' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Reciprocal Smallest Distance on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=reciprocal_smallest_distance
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers reciprocal_smallest_distance
rsd_search
-q Mycoplasma_genitalium.aa \
--subject-genome=Mycobacterium_leprae.aa \
-o Mycoplasma_genitalium.aa_Mycobacterium_leprae.aa_0.8_1e-5.orthologs.txt
rsd_format -g Mycoplasma_genitalium.aa
rsd_blast -v -q Mycoplasma_genitalium.aa \
--subject-genome=Mycobacterium_leprae.aa \
--forward-hits q_s.hits --reverse-hits s_q.hits \
--no-format --evalue 0.1