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TACOA specifications

Information


Unique identifier OMICS_01467
Name TACOA
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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Publication for TACOA

TACOA in pipeline

2015
PMCID: 4309676
PMID: 25673967
DOI: 10.4137/EBO.S20523

[…] to evaluate our method. firstly, we performed experiments to predict the unknown organisms of simulated metagenomes and compared our results with three other methods, phylopythias,10 phymm,11 and tacoa,12 at the lower taxonomic level. then, we used wsvdd’s training models to analyze the microbial diversity of five real human gut metagenomes. lastly, we evaluated the effectiveness of outliers […]


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TACOA in publications

 (13)
PMCID: 5767322
PMID: 29375610
DOI: 10.3389/fpls.2017.02241

[…] (xia et al., ). in compositional-based approaches, k-mer frequency measurements are used to classify metagenomic reads. methods such as tetra (teeling et al., ), compostbin (chatterji et al., ) and tacoa (diaz et al., ) organize sequences in clusters (k-mer frequency is used to build a feature vector to compute distances between reads). next, they assign an unique taxon to each cluster […]

PMCID: 4828583
PMID: 27148174
DOI: 10.3389/fmicb.2016.00469

[…] and accurate, but suffer primarily due to the time required to generate the blast or blat alignments. the composition-based or marker-gene based approaches, such as phylopythia (mchardy et al., ), tacoa (diaz et al., ), phymmbl (brady and salzberg, ), and metaphlan (segata et al., ) are several times faster in execution but provide limited classification accuracy and efficiency. however, given […]

PMCID: 4634789
PMID: 26537885
DOI: 10.1186/s12859-015-0788-5

[…] and s2) were computed on the metasimhc dataset with no clade exclusion. results were as expected, with all methods generally showing a relatively high sensitivity and precision. the exceptions are tacoa [], which is known to perform poorly on short reads, and metaphyler, which is a marker based method and thus only classifies a small proportion of the reads, resulting in low sensitivity (but […]

PMCID: 4309676
PMID: 25673967
DOI: 10.4137/EBO.S20523

[…] using generic features such as their 16s rrna, gc content, and other oligonucleotide frequencies.8 currently, there are several composition-based methods: phylopythia,9 phylo-pythias,10 phymm,11 tacoa,12 s-gsom,13 nbc,14 raiphy,15 knnlog,16 taxsom,17 and metacluster 3.0.18 however, at lower taxonomic levels, such as genus and species levels, most of these composition-based methods cannot […]

PMCID: 4091873
PMID: 25010839
DOI: 10.1371/journal.pone.0101021

[…] ∼300 times faster . metacv is a novel tool that applies a composition vector method to the amino acid space. such methods are well established for nucleotide-nucleotide comparisons (e.g. s-gsom or tacoa ), but novel for protein sequences., an average annotation rate of 32% was observed at the genus level despite the increasing number of sequenced microbial genomes (1,691 in reference database […]


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TACOA institution(s)
Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

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