Khmer

Description

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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. Template:App Location

Available versions

• 20120321 (Khmer is only distributed via a git repository, so versioning at HPC is by the snapshot dates).

Running the application using modules

To use khmer with the environment modules system at HPC the following commands are available:

Get module information for khmer:

$module spider khmer

Load the default application module:

$module load khmer

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_KHMER_DIR - directory where khmer is located.
• 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