RawGeno specifications

Information


Unique identifier OMICS_13872
Name RawGeno
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data A PeakScanner file
Input format TXTAll platforms
Operating system Unix/Linux
Programming languages R
License GNU General Public License version 2.0
Computer skills Medium
Version 2.0.1
Stability Alpha
Requirements
PeekScanner
Maintained Yes

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Publication for RawGeno

RawGeno in publications

 (12)
PMCID: 5936936
PMID: 29765671
DOI: 10.1098/rsos.172185

[…] georgia genomics facility (university of georgia) for fragment analysis on an abi 3130xl. we used peakscanner v. 1.0 (applied biosystems) to analyse resultant gel files and define fragment sizes and rawgeno [] to define particular bands. we duplicated the entire protocol for at least two individuals from each location to identify bands that consistently occurred and we eliminated bands […]

PMCID: 5622125
PMID: 28963513
DOI: 10.1038/s41598-017-10861-6

[…] of amplicon size categories and how the genotyping error per primer was calculated can be found in additional supporting information. the scoring of electropherograms was performed using the package rawgeno (v. 2.0.2) in r (v. 3.2.5) and rstudio (v. 1.0.136),. further msap analyses were performed using the r package msap (v. 1.1.9) following a band-based strategy. the bands were scored […]

PMCID: 5598967
PMID: 28910307
DOI: 10.1371/journal.pone.0184259

[…] is also affected by the software and selection criteria settings used []. for this reason, eight datasets were created in order to evaluate the influence of at least some of these parameters. rawgeno v2.0 [] with different settings was used to generate the first four datasets (“rawgeno” datasets) and the remaining datasets (“error” datasets) were created by combining procedures in rawgeno […]

PMCID: 5468153
PMID: 28616163
DOI: 10.1002/ece3.2751

[…] aflp electropherograms using peakscanner v1.0 (applied biosystems) with light peak smoothing and default settings. we analyzed results from peakscanner using a modified version of the r package rawgeno (arrigo, tuszynski, ehrich, gerdes & alvarez, ). for analyses of individual sets, we set the maximum bin width to two base pairs (bp), minimum bin width to one bp, minimum fragment size […]

PMCID: 5057222
PMID: 27724874
DOI: 10.1186/s12862-016-0773-2

[…] as well as the scoring approach followed rešetnik et al. []; electropherograms were analysed with peak scanner version 1.0 (applied biosystems), and automated binning and scoring was performed using rawgeno version 2.0 [], a package for the software r []., the error rate [] was calculated as the ratio of mismatches (scoring of 0 vs. 1) over phenotypic comparisons in aflp profiles of 43 […]


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RawGeno institution(s)
Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland; Science Applications International Corporation (SAIC), McLean, VA, USA; Department of Biology, University of Tromsø, Tromsø, Norway; Chromosome Laboratory, Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark; Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
RawGeno funding source(s)
This study was funded by the National Centre of Competence in Research (NCCR) Plant Survival and the Swiss National Science Foundation (project No. 3100A0-116778/1).

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