funannotate
Link to section 'Introduction' of 'funannotate' Introduction
Funannotate is a genome prediction, annotation, and comparison software package.
Docker hub: https://hub.docker.com/r/nextgenusfs/funannotate and its home page on Github.
Link to section 'Versions' of 'funannotate' Versions
- 1.8.10
Link to section 'Commands' of 'funannotate' Commands
- funannotate
Link to section 'Module' of 'funannotate' Module
You can load the modules by:
module load biocontainers
module load funannotate
Link to section 'Example job' of 'funannotate' 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 Funannotate on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=funannotate
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers funannotate
funannotate clean -i genome.fa -o genome_cleaned.fa
funannotate sort -i genome_cleaned.fa -o genome_cleaned_sorted.fa
funannotate predict -i genome_cleaned_sorted.fa -o predict_out --species "arabidopsis" --rna_bam RNAseq.bam --cpus 12