Khmer

Introduction

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

For more information, please check its website: https://biocontainers.pro/tools/khmer and its home page on Github.

Versions

  • 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:

#!/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