Khmer

Introduction

Khmer is a tool for k-mer counting, filtering, and graph traversal FTW!

For more information, please check:

BioContainers: https://biocontainers.pro/tools/khmer

Home page: https://github.com/dib-lab/khmer

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster	Version(s)
ANVIL	3.0.0a3
BELL	3.0.0a3
GAUTSCHI	3.0.0a3
NEGISHI	3.0.0a3
SCHOLAR	3.0.0a3

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

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 khmer on our clusters:

Anvil

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition 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
module biocontainers khmer

# Your khmer workflow...

Bell, Gautschi, or Negishi

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers khmer

# Your khmer workflow...

Gautschi-AI

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers khmer

# Your khmer workflow...

Gilbreth

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers khmer

# Your khmer workflow...

Scholar

#!/bin/bash
#SBATCH -A queue     # Queue 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
module biocontainers khmer

# Your khmer workflow...