Evaluation data for "GeFaST: An improved method for OTU assignment by generalising Swarm's fastidious clustering approach"

Müller R, Nebel M (2017) : Bielefeld University. doi:10.4119/unibi/2915656.

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Abstract
Data sets and results of the comparative analyses of [GeFaST](https://github.com/romueller/gefast) and [Swarm](https://github.com/torognes/swarm/) performed in "GeFaST: An improved method for OTU assignment by generalising Swarm's fastidious clustering approach" (submitted). The scripts for the analyses are available [here](https://github.com/romueller/gefast-paper-analysis).

**dereplicated.tar.bz2**: Data sets used in the analyses of performance (_ELDERMET_ [1]) and clustering quality (_even_ & _uneven_ [2]). The original data sets (see below) have been dereplicated and sequences containing ambiguous bases (IUPAC code _n_ resp. _N_) have been deleted.
* _even_: [http://sbr2.sb-roscoff.fr/download/externe/de/fmahe/even.fasta.bz2](http://sbr2.sb-roscoff.fr/download/externe/de/fmahe/even.fasta.bz2) * _uneven_: [http://sbr2.sb-roscoff.fr/download/externe/de/fmahe/uneven.fasta.bz2](http://sbr2.sb-roscoff.fr/download/externe/de/fmahe/uneven.fasta.bz2) * _ELDERMET_: [http://www.ebi.ac.uk/ena/data/view/SRP003158](http://www.ebi.ac.uk/ena/data/view/SRP003158) The analysis of the clustering quality also requires the [reference data set](https://raw.githubusercontent.com/torognes/vsearch-eval/master/cluster/data/rrna_reference.fasta).

**eldermet\_subsamples\_X.tar.bz2**: Each archive contains three random subsamples of _ELDERMET_ of size X, with X being the percentage of sequences from _eldermet\_derep.fasta_ (in _dereplicated.tar.bz2_) in the subsample.

**results.tar.bz2**: Results files containing the measurements of performance resp. clustering quality.
* _eldermet-performance-measurements.csv_: runtime and memory consumption for different thresholds * _eldermet-subsampling-measurements.csv_: runtime and memory consumption for different data set sizes * _even-metrics.csv_: clustering quality for different thresholds. * _uneven-metrics.csv_: clustering quality for different thresholds

References: [1] Claesson M.J., Cusack S., O'Sullivan O., Greene-Diniz R., de Weerd H., Flannery E., Marchesi J.R., Falush D., Dinan T., Fitzgerald G., Stanton C., van Sinderen D., O'Connor M., Harnedy N., O'Connor K., Henry C., O'Mahony D., Fitzgerald A.P., Shanahan F., Twomey C., Hill C., Ross R.P., O'Toole P.W.: Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proceedings of the National Academy of Sciences 108 (Supplement 1), 4586-4591 (2011). doi: [10.1073/pnas.1000097107](https://doi.org/10.1073/pnas.1000097107) [2] Mahé F., Rognes T., Quince C., de Vargas C., Dunthorn M.: Swarm: robust and fast clustering method for amplicon-based studies. PeerJ 2, 593 (2014). doi: [10.7717/peerj.593](https://doi.org/10.7717/peerj.593)
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This Evaluation data for "GeFaST: An improved method for OTU assignment by generalising Swarm's fastidious clustering approach" is made available under the Open Database License: http://opendatacommons.org/licenses/odbl/1.0. Any rights in individual contents of the database are licensed under the Database Contents License: http://opendatacommons.org/licenses/dbcl/1.0/
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Müller R, Nebel M. (2017): Evaluation data for "GeFaST: An improved method for OTU assignment by generalising Swarm's fastidious clustering approach". Bielefeld University. doi:10.4119/unibi/2915656.
Müller, R., & Nebel, M. (2017). Evaluation data for "GeFaST: An improved method for OTU assignment by generalising Swarm's fastidious clustering approach". Bielefeld University. doi:10.4119/unibi/2915656
Müller, R., and Nebel, M. (2017). Evaluation data for "GeFaST: An improved method for OTU assignment by generalising Swarm's fastidious clustering approach". Bielefeld University. doi:10.4119/unibi/2915656.
Müller, R., & Nebel, M., 2017. Evaluation data for "GeFaST: An improved method for OTU assignment by generalising Swarm's fastidious clustering approach". Bielefeld University. doi:10.4119/unibi/2915656
R. Müller and M. Nebel, Evaluation data for "GeFaST: An improved method for OTU assignment by generalising Swarm's fastidious clustering approach". Bielefeld University, 2017. doi:10.4119/unibi/2915656.
Müller, R., Nebel, M.: Evaluation data for "GeFaST: An improved method for OTU assignment by generalising Swarm's fastidious clustering approach". Bielefeld University (2017). doi:10.4119/unibi/2915656.
Müller, Robert, and Nebel, Markus. Evaluation data for "GeFaST: An improved method for OTU assignment by generalising Swarm's fastidious clustering approach". Bielefeld University, 2017. doi:10.4119/unibi/2915656
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