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


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Maintainer


  • person_outline Jacques Rougemont <>

Publication for Rolexa

Rolexa in publications

 (5)
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 […]

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). […]

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 […]

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, […]

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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