Difference between revisions of "Khmer"
Moskalenko (talk | contribs) m (Text replace - "Usage policy" to "Usage Policy") |
Moskalenko (talk | contribs) m (Text replace - "{{#if: {{#var: mod}}|==Execution Environment and Modules== {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}" to "==Required Modules== modules documentation ===Serial=== *{{#var:app}}") |
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* HPC_KHMER_BIN - directory where the scripts are located | * HPC_KHMER_BIN - directory where the scripts are located | ||
* HPC_KHMER_DOC - khmer documents are in this directory | * HPC_KHMER_DOC - khmer documents are in this directory | ||
Revision as of 16:55, 10 August 2012
Description
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.
IMPORTANT NOTE:
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
Serial
- 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