Difference between revisions of "Khmer"

Jump to navigation Jump to search
m (Text replace - "<!--Choose sections to enable - OPTIONAL--> |{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->" to "")
m (Text replace - "|{{#vardefine:intel|}} <!-- E.g. "11.1" --> |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->" to "")
Line 8: Line 8:
<!--Compiler and MPI settings - OPTIONAL -->
<!--Compiler and MPI settings - OPTIONAL -->
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->

Revision as of 17:53, 10 August 2012


khmer website  

Khmer - python scripts for k-mer counting, filtering and graph traversal.

There's a khmer mailing list at librelist.com that you can use to get help with khmer. To sign up, email 'khmer@librelist.com' to subscribe; then send your question/comment there.


khmer is *pre-publication* and *research* software, so please keep in mind that (a) the code may have undiscovered bugs in it, (b) you should cite us, and (c) you should get in touch if you need to cite us, as we are writing up the project.

Available scripts: abundance-dist.py, count-median.py, do-partition.sh, filter-abund.py, find-knots.py, load-into-counting.py, merge-partitions.py, normalize-by-median.py, partition-graph.py, annotate-partitions.py, count-overlap.py, extract-partitions.py, filter-stoptags.py, load-graph.py, make-initial-stoptags.py, normalize-by-kadian.py, normalize-by-min.py

To use the khmer module make sure python/2.7.2 is loaded and use "import khmer" in your script or in an interactive python session.

Required Modules

modules documentation


  • khmer
  • HPC_KHMER_BIN - directory where the scripts are located
  • HPC_KHMER_DOC - khmer documents are in this directory
  • HPC_KHMER_DATA - sample datasets are in this directory