Taxator-tk statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Taxator-tk
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Tool usage distribution map

This map represents all the scientific publications referring to Taxator-tk per scientific context
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Protocols

Taxator-tk specifications

Information


Unique identifier OMICS_06382
Name Taxator-tk
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Publication for Taxator-tk

Taxator-tk citations

 (6)
library_books

Investigation of different nitrogen reduction routes and their key microbial players in wood chip driven denitrification beds

2017
Sci Rep
PMCID: 5716999
PMID: 29208961
DOI: 10.1038/s41598-017-17312-2

[…] unctional annotation of the assembled genes was performed using GhostKOALA and Paladin v1.3.1. Taxonomic assignments were carried out using the BLASTN-based taxonomic binning algorithm implemented in taxator-tk v1.3.3. […]

library_books

TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms

2017
BMC Genomics
PMCID: 5644092
PMID: 29037173
DOI: 10.1186/s12864-017-4168-6

[…] ion of specific organisms in a sample, e.g. related to a disease.Another category of tools searches the NCBI database to assign reads to a taxonomic level after a BLAST search, including MEGAN [] and Taxator-tk [] or after a mapping with Bowtie2, e.g. Centrifuge [].For our purposes, we found that each existing tool exhibited a shortcoming that rendered it unsuitable for the read-level assignment o […]

library_books

Lignocellulose Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass Degrading Diversity

2017
PMCID: 5541161
PMID: 28776044
DOI: 10.1128/mSphere.00300-17

[…] fill sites.Developments in taxonomic binning of metagenome data sets have transformed our ability to assign functional attributes of mixed microbial communities to specific taxa (). Here, we utilized Taxator-tk to generate phylum-level taxonomic bins containing metagenome contigs for gene annotation and CAZyme profiling of each phylum. Phylum-level bins derived from the metagenome data set reveale […]

library_books

Characterisation of a stable laboratory co culture of acidophilic nanoorganisms

2017
Sci Rep
PMCID: 5468238
PMID: 28607432
DOI: 10.1038/s41598-017-03315-6

[…] ferent archaea. Hence the CARD-FISH analysis using archaea probes displayed the presence of two different organisms. Supplementary Figure  shows the taxonomic profiles for metagenomes determined with Taxator-tk. These profiles corroborate the CARD-FISH results and reveal that the majority of the available sequence (∼80%) can be assigned to the archaea, while the remaining part cannot be assigned t […]

call_split

Complete Genome Sequence of Aggregatibacter actinomycetemcomitans Strain IDH781

2016
Genome Announc
PMCID: 5105115
PMID: 27834722
DOI: 10.1128/genomeA.01285-16
call_split See protocol

[…] %, consistent with other completed A. actinomycetemcomitans genomes. To verify strain identity and detect possible horizontal gene transfer events, genomic intervals were taxonomically assigned using Taxator-tk (version 1.3.1e) with the nonredundant-microbial_20140513 database (refpack from http://research.bifo.helmholtz-hzi.de/software) (). All classified regions (39.8% of the genome) were assign […]

library_books

An evaluation of the accuracy and speed of metagenome analysis tools

2016
Sci Rep
PMCID: 4726098
PMID: 26778510
DOI: 10.1038/srep19233

[…] ndance of 16S rRNA genes is used to infer the gene content of the metagenome samples, taking into account the copy number of 16S genes. The final functional prediction is based on the KEGG Orthology. Taxator-tk: taxator-tk can use BLASTN or LAST to search with the reads against a local reference database. Overlapping local alignments between the read and a number of reference sequences are joined […]


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Taxator-tk institution(s)
Department for Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany; Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, Saarbrücken, Germany; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany

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