De Vargas, Colomban; Bittner, Lucie (2010): Svalbard 2010 mesocosm experiment: Protistan diversity [dataset]. Station Biologique de Roscoff, PANGAEA, https://doi.org/10.1594/PANGAEA.777733, In: Svalbard 2010 team (2010): EPOCA Svalbard 2010 mesocosm experiment in Kongsfjorden, Svalbard, Norway [dataset publication series]. PANGAEA, https://doi.org/10.1594/PANGAEA.769833
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Abstract:
Hierarchical clustering. Taxonomic assignment of reads was performed using a preexisting database of SSU rDNA sequences from including XXX reference sequences generated by Sanger sequencing. Experimental amplicons (reads), sorted by abundance, were then concatenated with the reference extracted sequences sorted by decreasing length. All sequences, experimental and referential, were then clustered to 85% identity using the global alignment clustering option of the uclust module from the usearch v4.0 software (Edgar, 2010). Each 85% cluster was then reclustered at a higher stringency level (86%) and so on (87%, 88%,…) in a hierarchical manner up to 100% similarity. Each experimental sequence was then identified by the list of clusters to which it belonged at 85% to 100% levels. This information can be viewed as a matrix with the lines corresponding to different sequences and the columns corresponding to the cluster membership at each clustering level. Taxonomic assignment for a given read was performed by first looking if reference sequences clustered with the experimental sequence at the 100% clustering level. If this was the case, the last common taxonomic name of the reference sequence(s) within the cluster was used to assign the environmental read. If not, the same procedure was applied to clusters from 99% to 85% similarity if necessary, until a cluster was found containing both the experimental read and reference sequence(s), in which case sequences were taxonomically assigned as described above.
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Parameter(s):
| # | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
|---|---|---|---|---|---|---|
| 1 | Sample ID | Sample ID | Bittner, Lucie | |||
| 2 | Experimental treatment | Exp treat | Bittner, Lucie | |||
| 3 | Experiment day | Exp day | day | Bittner, Lucie | ||
| 4 | Fraction | Fraction | Bittner, Lucie | |||
| 5 | Sequence abundance | sequence abund | # | Bittner, Lucie | ||
| 6 | Number of sequences | Sequence no | # | Bittner, Lucie | ||
| 7 | Fraction of sample | Fraction sample | # | Bittner, Lucie | ||
| 8 | Kingdom | Kingdom | Bittner, Lucie | |||
| 9 | Phylum | Phylum | Bittner, Lucie | |||
| 10 | Class | Class | Bittner, Lucie | |||
| 11 | Order | Order | Bittner, Lucie | |||
| 12 | Family | Family | Bittner, Lucie |
License:
Creative Commons Attribution 3.0 Unported (CC-BY-3.0)
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93578 data points
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