Software: dnaapler
Description
dnaapler is a simple python program that takes a single nucleotide input sequence (in FASTA format), finds the desired start gene using blastx against an amino acid sequence database, checks that the start codon of this gene is found, and if so, then reorients the chromosome to begin with this gene on the forward strand.
Available Versions
| Unspecified: | 0.1.0 |
|---|
Docker hub: https://hub.docker.com/r/staphb/dnaapler
Home page: https://github.com/gbouras13/dnaapler
Commands
- dnaapler
Module
You can load the modules by:
module load biocontainers
module load dnaapler
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
To run dnaapler on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=dnaapler
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers dnaapler