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