Difference between revisions of "Khmer"
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*{{#var:app}} | *{{#var:app}} | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{#uppercase:{{#var:app}}}}_DIR | + | * HPC_{{#uppercase:{{#var:app}}}}_DIR |
| − | * HPC_KHMER_BIN | + | * HPC_KHMER_BIN |
| − | * | + | * HPC_KHMER_LIB |
| − | |||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
Revision as of 13:47, 15 August 2014
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
Use "import khmer" in your script or in an interactive python session.
Required Modules
Serial
- khmer
System Variables
- HPC_{{#uppercase:khmer}}_DIR
- HPC_KHMER_BIN
- HPC_KHMER_LIB