Khmer pipeline

Khmer specifications


Unique identifier OMICS_02560
Name Khmer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Khmer team <>

Publications for Khmer

Khmer IN pipelines

PMCID: 5795050
PMID: 29321239
DOI: 10.1098/rsob.170184

[…] hiseq reads along with 2× 15 266 599 and 2× 16 274 715 gaiix reads. after trimming and cleaning (using tagcleaner [128] and prinseq [129]) of the data, we subsequently digitally normalized it with khmer [130] in order to discard redundant data and sampling variation and remove errors. this reduced the number of reads to 415 241 668 hiseq along with 28 964 302 and 30 961 514 gaiix, a reduction […]

PMCID: 4252092
PMID: 25461894
DOI: 10.1371/journal.pone.0114138

[…] adapter sequences and trimmed using adapterremoval v1.5.2 [30] and seqtk [31] and error corrected with quake v0.3 [32]. redundant reads were removed through digital normalization with diginorm in khmer v0.5 package [33]., the genomes were assembled to scaffolds with velvet v1.2.10 [34] or clc genomic workbench (clc bio, denmark). several k-mer sizes and coverage values were tested to obtain […]

Khmer institution(s)
Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
Khmer funding source(s)
Supported in part by the United States Department of Agriculture under grant 2009-03296 from the National Institute of Food and Agriculture, the National Science Foundation grant 09-23812, the National Institutes of Health grant 1R01HG007513-01 and NSF Postdoctoral Fellowship Award #0905961.

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