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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

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Documentation


Publication for Taxator-tk

Taxator-tk citations

 (8)
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

[…] 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., all data generated or analyzed during this study are included in this published article (and its supplementary information files). all dna and rna sequences that were retrieved […]

call_split

Draft Genome Sequences of Aggregatibacter actinomycetemcomitans Strains 310a and 310b

2017
Genome Announc
PMCID: 5701468
PMID: 29167243
DOI: 10.1128/genomeA.01282-17
call_split See protocol

[…] nonredundant-microbial_20140513 reference database using the dc-megablast algorithm with the taxator toolkit (v 1.3.3e) () (https://research.bifo.helmholtz-hzi.de//sotware; https://github.com/fungs/taxator-tk). all classified regions of both genomes belonged to the species aggregatibacter actinomycetemcomitans (11.47% for 310a and 11.31% for 310b). annotation was performed by ncbi using […]

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

[…] 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 […]

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

[…] 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 […]

library_books

Complete Genome Sequence of Aggregatibacter actinomycetemcomitans Strain IDH781

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

[…] 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) […]

library_books

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production scale biogas plants

2016
Biotechnol Biofuels
PMCID: 4960831
PMID: 27462367
DOI: 10.1186/s13068-016-0565-3

[…] [], using sets of clade-specific single-copy marker genes. genome bins of distinct taxa were identified by (a) counting the aforementioned taxonomic assignments on gene level, and (b) running taxator-tk (v1.2.1; binning-workflow-fasta-blast.sh) [] to additionally assign a taxon label on contig level. these two approaches were largely in agreement, identifying high-confident genome bins […]


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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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