Next-Generation Sequencing: From Basic Research to Diagnostics ...

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Supplemental Figure 1. SOLiD Color Space Coding and Sequence Deconvolution. Top. Left)Interrogation of a template with sequence TAGACA (positions 1-6 with adapter sequence T atposition 0). Right) Color space coding is reshown as reference. Bottom. Sequencing by ligationand deconvolution of template sequence. Extension of primer (n) interrogates template positions1 and 2, 6 and 7, 11 and 12, and so forth. No sequence information can be determined during thefirst round since each fluor represents four two base possible combinations. The extension ofprimer (n-1) allows for the deconvolution of the base at position 1 with the knowledge of the P1adapter base “T” at position 0. The extension of primers (n-2) and (n-3) provide additionalpositional color space information prior to deconvolution of the template performed after round 5(primer n-4). The ”N” bases show the positions along the template that have been sequencedtwice prior to deconvolution.
Supplementary Data Table 1 Next Generation Sequencing Software SummaryAlignment to ReferenceDe Novo AssemblySNP Indel DiscoveryCHiP/ Bisulphite -SeqRNA-SeqAlternate Base CallerAlignment ViewerStatistical AnalysisPrimaryOperatingProgram NameEnvironmentsALLPATHS X (1) Jonathan Butler et al.ReferencesAuthorsWeb SiteAlta-cyclic XLinux, SGE clusterenvironment(2) Yaniv Erlich et al. hannonlab.cshl.edu/Alta-Cyclic/main.htmlBowtie X Linux, Windows, Mac Ben Langmead and Cole Trapnell bowtie-bio.sourceforge.netepigenomics.mcdb.ucla.edu/BS-BS-Seq X POSIX OS (3) S.J. Cokus et alSeq/download.htmlCHiPSeq X Linux, Mac (4) D.S. Johnson et al. woldlab.caltech.edu/html/chipseq_peak_finderCLCbioGenomicsWorkbenchX X X X Windows CLCbio www.clcbio.comEagleView X Linux, Windows, Mac (5) W. Huang, G. Marth bioinformatics.bc.edu/marthlab/EagleViewEdena X Linux, Windows (6) www.genomic.ch/edena.phpELAND X Linux Anthony J. Cox bioinfo.cgrb.oregonstate.edu/docs/solexaErange X X Linux, Mac (7) Ali Mortazavi et al. woldlab.caltech.edu/rnaseqEuler-SR X (8, 9) Mark J. Chaisson and Pavel A. PevznerExonerate X Linux (10) Guy St, C Slater and Ewan Birney www.ebi.ac.uk/~guy/exonerateFindPeaks X Java (11) Anthony Fejes vancouvershortr.sourceforge.netGMAP X Unix (12) Thomas Wu and Colin WatanabeJMP Genomics X X Linux, Win, Mac SAS Institue Inc. www.jmp.com/software/genomicsMAQ X Linux, Mac (13) Heng Li maq.sourceforge.net/index.shtmlMIRA2 X X Linux (14) Bastien Chevreux chevreux.org/projects_mira.htmlMOSAIK X Michael Strömberg and Gabor MarthMUMmer X POSIX OS (15)Stefan Kurtz, Adam Phillippy, Arthur L Delcher, MichaelSmoot, Martin Shumway, Corina Antonescu and Steven L.Salzberghttp://mummer.sourceforge.netNextGENe X X X X Windows SoftGenetics www.softgenetics.comNOVOALIGN X Linux, Mac OS X Novocraft Technologies www.novocraft.com/products.htmlPBShort X Linux Gabor Marth bioinformatics.bc.edu/marthlab/PbShortPyroBayes X Linux (16) A.R. Quinlan, D.A. Stewart, M.P. Strömberg, G.T. Marth http://bioinformatics.bc.edu/marthlab/PyroBayes
Page 1 and 2: Clinical Chemistry 55:4641-658 (200
Page 4 and 5: ReviewsFig. 2. Illumina Genome Anal
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Page 8 and 9: ReviewsGENOMIC ANALYSISThe high-thr
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Page 14 and 15: Reviewstechnical procedures, robust
Page 16 and 17: Reviewsquirements: (a) significant
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Next-Generation Sequencing: From Basic Research to Diagnostics ...

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