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.

Versions

1.1.7

Commands

rsd_search
rsd_blast
rsd_format

Module

You can load the modules by:

module load biocontainers
module load reciprocal_smallest_distance

Example job

Warning

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