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Kmer specifications


Unique identifier OMICS_28964
Name Kmer
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


  • A2Amapper
  • LEAFF (Let’s Extract Anything From Fasta)
  • sim4db




No version available


  • person_outline Liliana Florea

Publication for Kmer

Kmer citations


Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

PMCID: 5801463
PMID: 29437920
DOI: 10.1128/mBio.02011-17
call_split See protocol

[…] ng a k-mer inclusion approach. Briefly, 16-bp k-mers were generated from the fully resolved PacBio plasmid sequences along with the MiSeq genome assemblies by using meryl (13 May 2015 release, A plasmid was considered present within a genome assembly if ≥95% of the plasmid k-mers were contained within the MiSeq genome assembly k-mers. A similar k-mer inclusion analys […]


Range expansion underlies historical introgressive hybridization in the Iberian hare

Sci Rep
PMCID: 5264399
PMID: 28120863
DOI: 10.1038/srep40788

[…] addition, low frequency variants were filtered out, retaining only sites with a minimum allele frequency of 0.2.Spliced alignments of the assembled contigs with the rabbit genome were produced using sim4db v1.896 in order to identify intron-exon boundaries. Only sequences with more than 90% identity and SNPs laying within the inferred alignment coordinates were retained for further analyses.One f […]


Transcriptome analysis of root response to citrus blight based on the newly assembled Swingle citrumelo draft genome

BMC Genomics
PMCID: 4938905
PMID: 27391971
DOI: 10.1186/s12864-016-2779-y

[…] nce-based approach []. The completeness and accuracy of the coding region of the draft assembly were validated using the Core Eukaryotic Genes Mapping Approach (CEGMA) [] as well as EST mapping using sim4db and exonerate [, ], respectively. The annotation of this draft genome was created using MAKER2 pipeline []. The detailed genome assembly and annotation pipeline are listed in the Additional fil […]


Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement

Sci Rep
PMCID: 4663792
PMID: 26617401
DOI: 10.1038/srep17394

[…] low copy regions, such as those rich in gene content. This is supported by the gene annotations and the K-mer spectras of reads for the different assemblies (). In these figures, the areas under the Kmer spectra were coloured according to the number of times that such Kmers appeared in each assembly. Approximately 173, 74 and 41 Mb appeared once, twice and more than twice in the Platanus assembly […]


Pathogen regulated genes in wheat isogenic lines differing in resistance to brown rust Puccinia triticina

BMC Genomics
PMCID: 4595183
PMID: 26438375
DOI: 10.1186/s12864-015-1932-3

[…] g (unique transcripts) assembly along with transcriptomic data (EST, cDNA) from GenBank with the CAP3 program []. All EST clusters were validated by similarity search to wheat genome using BLASTn and sim4db tools [, ]. Transcripts showing at least 90 % coverage and 80 % similarity were considered as originating from wheat. Remaining, non-mapping sequences were compared to fungi genomic databases ( […]


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