khmer
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'khmer' Versions
- 3.0.0a3
Link to section 'Commands' of 'khmer' 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
Link to section 'Module' of 'khmer' Module
You can load the modules by:
module load biocontainers
module load khmer
Link to section 'Example job' of '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