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Taxy specifications

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Unique identifier OMICS_10703
Name Taxy
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data As input, DNA sequences in terms of multi-FASTA files of any size can be used for the estimation of metagenomic profiles.
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Peter Meinicke <>

Publication for Taxy

Taxy citations

 (3)
library_books

Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries

2015
PMCID: 4459075
PMID: 26056565
DOI: 10.1186/s40168-015-0086-5

[…] bias occurs post size selection, we next asked if certain taxa were differentially represented across the samples to see if this would point to a possible reason for library sequence bias. we used taxy [] as well as taxy-pro [] as part of the comet web server [] to do a fast preliminary comparison of taxa abundance across the three different samples. taxy calculates k-mer frequencies […]

library_books

Exploring Neighborhoods in the Metagenome Universe

2014
PMCID: 4139848
PMID: 25026170
DOI: 10.3390/ijms150712364

[…] can be detected by all methods. here, the metaphlan and mop-pro methods show very little variation of the accuracy with respect to the underlying profile distance measure. on the other side, taxy-oligo and go show a relatively low accuracy on average and are much more susceptible with respect to the distance metric. the go slim profile space has the lowest dimensionality and it seems […]

library_books

Microbiota Present in Cystic Fibrosis Lungs as Revealed by Whole Genome Sequencing

2014
PMCID: 3944733
PMID: 24599149
DOI: 10.1371/journal.pone.0090934

[…] to assign a taxon to each matching read. the two other methods, metaphlan and metaphyler, consisted in searching for clade-specific marker genes. in addition, we tried the composition-based method taxy designed to be used with short reads , but it did not produce convincing results. indeed, different results were obtained whether it was applied on complete or filtered datasets, […]


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Taxy institution(s)
Department of Bioinformatics, Institute for Microbiology and Genetics, Georg-August University, Göttingen, Germany
Taxy funding source(s)
Grants from the Deutsche Forschungsgemeinschaft (ME 3138, ‘Compositional descriptors for large scale comparative metagenome analysis’ and LI 2050, ‘Development of machine learning methods for functional characterization of the peroxisome’)

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