Khmer protocols

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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



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  • person_outline Khmer team <>

Publications for Khmer

Khmer in pipelines

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

[…] 760 559 hiseq reads along with 2× 15 266 599 and 2× 16 274 715 gaiix reads. after trimming and cleaning (using tagcleaner [] and prinseq []) of the data, we subsequently digitally normalized it with khmer [] 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: 5831733
PMID: 29490679
DOI: 10.1186/s13059-018-1402-8

[…] selected fractions for sequencing. at the time of sequencing, illumina hiseq 2500 was the best sequencing platform available. joining all the reads from each sequenced sample and following the khmer-protocols v0.84 [], we assembled a reference transcriptome that would reflect all protein-coding genes expressed in the analysed stages (fig. ). in this three-step assembly, we first trimmed […]

PMCID: 5230755
PMID: 28081123
DOI: 10.1371/journal.pntd.0005216

[…] filtering off exogenous and/or non-confident bases (options:–q 13, -l 30, -p 80) within fastq files were performed with alientrimmer []. redundant or over-represented reads were reduced using the khmer software package (option:–c 70) []. finally, sequencing errors were corrected using musket [] and overlapping paired reads were merged with flash []. a de novo assembly was performed […]

PMCID: 5418858
PMID: 28472930
DOI: 10.1186/s12864-017-3729-z

[…] score at least 30 (q30)., raw reads were subject to host dna contamination removal with deconseq [] followed by a three-way protocol for digital normalization of high coverage libraries using khmer perl scripts []. resulting reads were assembled with mira 4 (mode: genome, accurate, others parameters default) [] and final genomes were assessed by manual inspection of coverage and mapping […]

PMCID: 5477187
PMID: 28473379
DOI: 10.1128/genomeA.00262-17

[…] trimmed to remove low-quality ends (<15) and adapters, using trimmomatic (version 0.36) (). to remove contaminant sequences or sequence errors, reads with low coverage (<5×) were removed using khmer (version 2.0) (), resulting in 1,084,068 high-quality reads (542,034 pairs) totaling 266 mb (~84-fold coverage). the high-quality reads were further assembled using spades version 3.9.0 (), […]

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Khmer in publications

PMCID: 5941587
PMID: 29739433
DOI: 10.1186/s12992-018-0361-x

[…] arguments that they are “undeserving” [, ], which usually leads to high rates of self-treatment or use of private clinics [, ]. among migrant fishermen in thailand, higher proportions of burmese and khmer fishermen self-treated compared to thai fishermen []., migrant fishermen in thailand can enrol in the health insurance card scheme (hics), administered the ministry of public health (moph). […]

PMCID: 5934858
PMID: 29724181
DOI: 10.1186/s12884-018-1768-3

[…] south wales (unsw) in australia., the study design and recruitment procedures are described in detail elsewhere []. briefly, eligibility criteria included: being biologically female (aged 15–29), khmer language comprehension, working in a sex work or entertainment venue and having two or more sexual partners in the last month or engaging in transactional sex (defined as having exchanged sex […]

PMCID: 5915733
PMID: 29691339
DOI: 10.1128/mBio.00573-18

[…] reads were clipped and trimmed with alientrimmer v.0.4.0 (), corrected with musket v.1.1 (), merged (if needed) with flash v.1.2.11 (), and subjected to a digital normalization procedure with khmer v.2.0 (). for each sample, processed reads were finally assembled with spades v.3.10 ()., for each pair of assembled genomes, an evolutionary distance (proportion of aligned nucleotide […]

PMCID: 5879732
PMID: 29609547
DOI: 10.1186/s12875-018-0728-3

[…] 35% of the population reporting english as their second language (up to 70% in some suburban areas). other than english, the main languages spoken in the area include arabic, chinese, vietnamese, khmer, korean, greek, spanish, italian and serbian. unemployment rates are high in the area (5.2 to 22.3% as compared to the nsw average of 4.7%), and median individual incomes for over a third […]

PMCID: 5879807
PMID: 29609580
DOI: 10.1186/s12906-018-2181-1

[…] population ranged from 26% to 52% []., cambodia offers a unique opportunity to examine the sociocultural, economic and medical reasons in patients who utilize tcam. between 1975 and 1979, the khmer rouge killed or detained physicians and closed the cambodia’s only medical school; by 1979, only 45 western-medicine-trained physicians remained in the country []. as a result, cambodia has one […]

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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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