Purdue University

Commands

• abundance-dist.py
• abundance-dist-single.py
• annotate-partitions.py
• count-median.py
• cygdb
• cython
• cythonize
• do-partition.py
• extract-long-sequences.py
• extract-paired-reads.py
• extract-partitions.py
• fastq-to-fasta.py
• filter-abund.py
• filter-abund-single.py
• filter-stoptags.py
• find-knots.py
• interleave-reads.py
• load-graph.py
• load-into-counting.py
• make-initial-stoptags.py
• merge-partitions.py
• normalize-by-median.py
• partition-graph.py
• readstats.py
• sample-reads-randomly.py
• screed
• split-paired-reads.py
• trim-low-abund.py
• unique-kmers.py

Module

You can load the modules by:

module load biocontainers
module load khmer

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 Khmer on our clusters:

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

module --force purge
ml biocontainers khmer