atram
aTRAM (automated target restricted assembly method) is an iterative assembler that performs reference-guided local de novo assemblies using a variety of available methods.
Detailed usage can be found here: https://bioinformaticshome.com/tools/wga/descriptions/aTRAM.html
Link to section 'Versions' of 'atram' Versions
- 2.4.3
Link to section 'Commands' of 'atram' Commands
- atram.py
- atram_preprocessor.py
- atram_stitcher.py
Link to section 'Module' of 'atram' Module
You can load the modules by:
module load biocontainers
module load atram/2.4.3
Link to section 'Example job' of 'atram' 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 aTRAM on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=atram
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers atram/2.4.3a
atram_preprocessor.py --blast-db=atram_db \
--end-1=data/tutorial_end_1.fasta.gz \
--end-2=data/tutorial_end_2.fasta.gz \
--gzip
atram.py --query=tutorial-query.pep.fasta \
--blast-db=atram_db \
--output=output \
--assembler=velvet