khmer

 

The khmer software is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. 

Documentation

 

Usage on Bridges

 

khmer is part of the Python package on Bridges. To use it, load this python module:

module load python/2.7.11_gcc