Swift protocols

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Swift specifications

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Unique identifier OMICS_01157
Name Swift
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
Illumina Solexa
Maintained Yes

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Publication for Swift

Swift in pipeline

2012
PMCID: 3438129
PMID: 22838726
DOI: 10.1186/1471-2180-12-156

[…] china) for commercial sequencing. the whole genome sequence, with a total length of 166,682 bp, was obtained using the illumina solexa sequencing platform (illumina, san diego, usa) and the swift analysis tool (http://swiftng.sourceforge.net) []. the genome sequence was analyzed with the ncbi blastx bioinformatics tool (http://blast.ncbi.nlm.nih.gov/blast.cgi) for nucleotide analysis, […]


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Swift in publications

 (2)
PMCID: 3178052
PMID: 21245079
DOI: 10.1093/bib/bbq077

[…] the intensity data needs to be extracted from the raw images before any of the above can be used. this image processing step is usually performed using bustard's firecrest module. bing [] and swift [] are alternative implementations of the complete data processing pipeline. both image processing algorithms differ in many mechanistic details from bustard. with bing, one has the option […]

PMCID: 2908109
PMID: 20598141
DOI: 10.1186/1756-0500-3-183

[…] (illumina, inc), developed specifically for performing three major functions: image analysis, base-calling and genome alignment. alternatives to the genomeanalyzer however do exist, such as swift []. by the end of the genomeanalyzer pipeline, the genomeanalyzer would have performed alignments with the sequenced reads and a reference genome with accompanying dna sequence quality scores […]


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Swift institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK; Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK; Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Harvard-Smithsonian Center for Astrophysics, MA, USA; Harvard Medical School, Genetics, Boston, MA, USA

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