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Rolexa specifications

Information


Unique identifier OMICS_01156
Name Rolexa
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format INT or CIF
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.26.0
Stability Stable
Requirements
methods, stats, graphics, IRanges, ShortRead, Biostrings, grDevices, mclust, R(>=2.9.0)
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Jacques Rougemont

Publication for Rolexa

Rolexa citations

 (5)
library_books

HIV protease inhibitors disrupt astrocytic glutamate transporter function and neurobehavioral performance

2016
PMCID: 4732003
PMID: 26558720
DOI: 10.1097/QAD.0000000000000955

[…] with a solution containing 127 mmol/l nacl, 2.5 mmol/l kcl, 1.2 mmol/l nah2po4, 1.3 mmol/l mgso4, 26 mmol/l nahco3, 25 mmol/l d-glucose and 2.5 mmol/l cacl2. images were recorded using a ccd camera (rolexa-xr f-m-12-c; qimaging, british columbia, canada) at 3 s/frame. selected regions of interest were drawn around distinct cells and traces of time course of average changes of fluorescent […]

library_books

Adult Zebrafish Hearts Efficiently Compensate for Excessive Forced Overload Cardiac Stress with Hyperplastic Cardiomegaly

2012
PMCID: 3559224
PMID: 23515072
DOI: 10.1089/biores.2012.0201

[…] extraction. ten ex and ten control were sacrificed for physiological contractile studies; nine ex and eight control were sacrificed for tissue sections., video images were recorded using a q-imaging rolexa-xr fast 1394 camera (q-imaging, surrey, canada) attached to a mz8 leica dissection scope (leica microsystems, inc., buffalo grove, il) with streampix software (norpix, montreal, canada). […]

library_books

Sequence specific error profile of Illumina sequencers

2011
Nucleic Acids Res
PMCID: 3141275
PMID: 21576222
DOI: 10.1093/nar/gkr344

[…] made to improve the error rate of the illumina sequencers. besides the improvement in experimental procedures, several base call programs have been developed. these include ibis, alta-cyclic and rolexa (,,). these programs consider a simple model for the regression of quality and improve base calls in terms of mismatch ratio. we examined the ibis base calls for phix and found […]

library_books

Base calling for next generation sequencing platforms

2011
Brief Bioinform
PMCID: 3178052
PMID: 21245079
DOI: 10.1093/bib/bbq077

[…] also requires resequencing part of a reference genome in order to generate enough training data. the ϕx174 control lane can be used for training., another approach is implemented in a package called rolexa []. like bustard, rolexa first applies a cycle dependent linear transform accounting for cross-talk between the different bases, before using a binomial distribution for dephasing. finally, […]

library_books

Detection of Genomic Variation by Selection of a 9 Mb DNA Region and High Throughput Sequencing

2009
PLoS One
PMCID: 2722027
PMID: 19684856
DOI: 10.1371/journal.pone.0006659

[…] match on the ucsc hg18 reference genome. the results, presented in , indicate that only 13% of the reads find an exact match, and 85% of the reads exhibit variants or sequencing errors. we then used rolexa software to improve the quality of the reads. the rolexa software pipeline utilizes the image intensity files produced by the illumina sequencing equipment and performs base calling […]


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Rolexa institution(s)
School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Ludwig Institute for Cancer Research (LICR), Université de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Université de Lausanne, Lausanne, Switzerland; Vital-IT, Université de Lausanne, Lausanne, Switzerland; Fasteris SA, Plan-les-Ouates, Switzerland
Rolexa funding source(s)
The Swiss National Science Foundation grant no 3100A0-113617

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