khmer.rst

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