Khmer statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Khmer

Tool usage distribution map

This map represents all the scientific publications referring to Khmer per scientific context
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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




No version available



  • person_outline Khmer team

Publications for Khmer

Khmer citations


Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab

PMCID: 5142744
PMID: 27942385
DOI: 10.5334/jors.35

[…] f scientific problems being studied with sequencing is driving the rapid development of many new tools, both for handling data on large scales and to address new and different biological problems.The khmer software was born from a need to more scalably analyze short fixed-length (20–30 character) words, or “k-mers”, in large DNA sequencing data sets. The use of k-mers in DNA sequence analysis is c […]


Conservation and diversification of the transcriptomes of adult Paragonimus westermani and P. skrjabini

PMCID: 5020434
PMID: 27619014
DOI: 10.1186/s13071-016-1785-x

[…] , bacteria [], Homo sapiens (GenBank version hs37) and Canis familiaris (GenBank version 3.1). Remaining high-quality, contaminant-free read sets were down-sampled by digital read normalization using khmer (k = 20) []. Reads selected in the down-sampling and their mates were assembled using the Trinity de novo RNA-Seq assembler using default parameters []. Scripts included in the Trinity software […]


Implementation research: a mentoring programme to improve laboratory quality in Cambodia

Bull World Health Organ
PMCID: 5043202
PMID: 27843164
DOI: 10.2471/BLT.15.163824

[…] ous forme de tableur en une liste de contrôle qui comprend un plan d'action détaillé et peut être utilisée pour contrôler, du point de vue qualitatif, la progression de chaque laboratoire. Traduit en khmer, il comprenait une série d'activités visant à améliorer la qualité, regroupées en quatre phases de mise en œuvre à complexité croissante. L'équipe du projet a examiné la progression et les diffi […]


Resolving the Complexity of Human Skin Metagenomes Using Single Molecule Sequencing

PMCID: 4752602
PMID: 26861018
DOI: 10.1128/mBio.01948-15

[…] . Sequencing depth was evaluated using k-mer accumulation. SMRT reads were split into 100-bp fragments using pyfasta 0.5.2. Reads were then split into k-mers, compared to a k-mer coverage table using khmer v0.7.1 (), and kept only if the median k-mer coverage was below a 5× cutoff. The resulting curves estimate the coverage of k-mer space as a function of sequencing effort.Matched 16S rRNA and ITS […]


Whole Genome Sequences of Three Symbiotic Endozoicomonas Bacteria

Genome Announc
PMCID: 4132622
PMID: 25125646
DOI: 10.1128/genomeA.00802-14

[…] reads were trimmed for quality, and the Illumina adapters were removed using Trimmomatic (). Fragments with both surviving read pairs were then digitally normalized using the recommended protocol in khmer (). The long mate-pair reads were trimmed using NextClip (), and fragments with the junction adapter in at least one of the paired reads were used in the assembly. The small- and long-insert lib […]


Influenza A(H5N1) Virus Surveillance at Live Poultry Markets, Cambodia, 2011

PMCID: 3559060
PMID: 23347451
DOI: 10.3201/eid1902.121201

[…] In 2011 in Cambodia, environmental samples were collected from 4 LPMs each week for 7 weeks, including during the Khmer New Year festival (). Two of the markets were in Phnom Penh, the capital city: Orussey market (M1) and Chamkar Doung market (M2), which also served as an overnight resting place and a place to k […]

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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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