TALLYMER protocols

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TALLYMER specifications


Unique identifier OMICS_02096
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for TALLYMER

TALLYMER in pipelines

PMCID: 4981986
PMID: 27519651
DOI: 10.1186/s12864-016-2980-z

[…] for further analysis., genome coverage in genes (cds) and transposable elements was calculated by 500 kb window with an overlap of 50 kb. genes and transposable elements (repet + repeatscout + tallymer) annotations and a karyotype were also needed., the resulting files were formatted to be visualized graphically through the circos software []. a clustering step of the different coverage […]

PMCID: 4508392
PMID: 26063859
DOI: 10.1128/JCM.00923-15

[…] genome (st. louis [stl] 2014 strain, genbank accession no. km881710.2). comprehensive k-mer analysis was performed on the database by indexing and reporting all 20-mer subsequences using the tallymer software (). we eliminated 20-mers that were not unique in the k-mer pool, thus leaving 20-mers that were unique to ev-d68 and those unique to other viral species. ev-d68-unique 20-mers […]

PMCID: 4085609
PMID: 24833511
DOI: 10.3390/biology3020295

[…] were also identified, and their relative abundance and density were determined. the frequencies of different ssr motifs within each di-, tri-, and tetranucleotide repeats were estimated as well. , tallymer [], a program based on enhanced suffix arrays [], was used to compute the 20-mer occurrence counts and construct a frequency index of each 20-mer. these frequencies were plotted […]

PMCID: 3213688
PMID: 21999860
DOI: 10.1186/1756-0500-4-411

[…] duplicons and reduced to only one pair. contig pairs that were supported by illumina mps were stored in a graph structure using java jung library., repeats were predicted by k-mer frequencies using tallymer []. the index of frequences was built from all reads of pool2., all reads from pool 2 were assembled without (non-bc) and after separation by barcodes using mira. read coverages […]

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TALLYMER in publications

PMCID: 5751119
PMID: 29186809
DOI: 10.3390/ijms18122516

[…] region from the sequences. after this pre-processing, a tool to count the sequence frequency is required. previously, aptamer research groups used genomic informatics software packages such as tallymer [,] or razers [,], or designed in-house programs to fulfill the counting requirement [,]. , galaxy project is a platform that provides fundamental bioinformatic tools for bench scientists […]

PMCID: 5778497
PMID: 29126307
DOI: 10.1093/nar/gkx1053

[…] that have the potential to be detected based on their unique genomic mappability when it calculates the expected k-mer detection frequency from the fasta file. seqoutbias invokes genometools’ tallymer to compute mappability at each position in the genome (,). first, the reference genome fasta file is indexed using genometools’ tallymer program (,). next, tallymer computes unique […]

PMCID: 5704207
PMID: 29068386
DOI: 10.3390/genes8110294

[…] fragment of length k. the method relies on the construction of a set of such k-mer indices covering all sequence motifs occurring in the dataset. two programs designed to perform this task are tallymer [] and jellyfish []. the kmasker tool [] can be applied to run the k-mer frequency ratio analysis. in addition to its core functionality of masking repetitive elements and identifying low […]

PMCID: 5555453
PMID: 28667019
DOI: 10.1534/g3.117.040907

[…] to the genomic sequences as a result of sequence improvement., repeat detector (red) () and windowmasker () were run against the improved d. ananassae assembly using default parameters. for the tallymer analysis (), the word sizes (k) of 17 and 19 were used to analyze the d. melanogaster and the d. ananassae assemblies, respectively (see “supplemental methods” in file s7 for the procedures […]

PMCID: 4981986
PMID: 27519651
DOI: 10.1186/s12864-016-2980-z

[…] library (repeatscout annotation). regions identified by the repeatscout approach that span at least 50 bp and that are not included in repet annotations (54 mb) were combined to the latter. tallymer was launched with a k-mer size = 16 and a minimum of 10 occurrences in the sl2.40 assembly. fragments of at least 30 bp that do not overlap the repet and repeatscout annotations were kept. […]

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TALLYMER institution(s)
Center for Bioinformatics, University of Hamburg, Hamburg, Germany; Cold Spring Harbor Lab, Cold Spring Harbor, NY, USA; Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA

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