Purdue University

Commands

• fa2fq
• filter_blat
• filter_contigs
• filterfa
• fq2fa
• idba
• idba_hybrid
• idba_tran
• idba_tran_test
• idba_ud
• parallel_blat
• parallel_rna_blat
• print_graph
• raw_n50
• run-unittest.py
• sample_reads
• scaffold
• scan.py
• shuffle_reads
• sim_reads
• sim_reads_tran
• sort_psl
• sort_reads
• split_fa
• split_fq
• split_scaffold
• test
• validate_blat
• validate_blat_parallel
• validate_component
• validate_contigs_blat
• validate_contigs_mummer
• validate_reads_blat
• validate_rna

Module

You can load the modules by:

module load biocontainers
module load idba

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 Idba on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=idba
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers idba

fq2fa --paired --filter SRR1977249.abundtrim.subset.pe.fq SRR1977249.abundtrim.subset.pe.fa
idba_ud  -r SRR1977249.abundtrim.subset.pe.fa -o output