aTRAM

Introduction

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

Versions

  • 2.4.3

Commands

  • atram.py

  • atram_preprocessor.py

  • atram_stitcher.py

Module

You can load the modules by:

module load biocontainers
module load atram/2.4.3

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 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