Using quality scores and longer reads improves accuracy of Solexa read mapping

Keywords

Computer science, Reference genome, Upload, DNA microarray, Deep sequencing

References

• Base-calling of automated sequencer traces using phred. I. Accuracy assessment.Анатольев Алексей Владимирович — 1998
• Algorithms on Strings, Trees, and Sequences - Computer Science and Computational BiologyDan Gusfield — 1997
• Hacker's DelightH. S. Warren — 2002
• Fast and Practical Approximate String MatchingRicardo Baeza‐Yates, Chris H. Perleberg — 1992
• High-resolution profiling of histone methylations in the human genome.Artem Barski, Suresh Cuddapah, Kairong Cui — 2007
• Genome-wide maps of chromatin state in pluripotent and lineage-committed cellsTarjei S. Mikkelsen, Manching Ku, David B. Jaffe — 2007
• Multiple filtration and approximate pattern matchingPavel A. Pevzner, Michael S. Waterman — 1995
• Basic local alignment search tool.Stephen F. Altschul, Warren Gish, Webb Miller — 1990
• Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencingGordon Robertson, Martin Hirst, Matthew N. Bainbridge — 2007
• Whole-genome re-sequencing.David Bentley — 2006
• Base-calling of automated sequencer traces using phred. II. Error probabilities.Brent Ewing, Phil Green — 1998
• Genome sequencing in microfabricated high-density picolitre reactorsMarcel Margulies, Michael D. Miller, William E. Altman — 2005
• PatternHunter: faster and more sensitive homology searchBin Ma, John Tromp, Ming Li — 2002
• Complete MHC haplotype sequencing for common disease gene mapping.Claudia Stewart, Roger W. Horton, Richard Allcock — 2004
• Algorithms on strings, trees, and sequencesDan Gusfield — 1997

Cited by

• High Performance Computing for DNA Sequence Alignment and AssemblySteven L. Salzberg, Michael C. Schatz — 2010
• Reduced Representation Bisulfite Sequencing of Human Neutrophils Reveals Widespread Inter-Individual Epigenetic VariationAniruddha Chatterjee — 2013
• FPGA-based acceleration of the RMAP short read mapping toolPooja Mhapsekar — 2013
• High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing.Thomas M. Brown, S. Baggett — 2009
• PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seedsVan Jacobson, Jerry Fiddler, J. Greer — 2009
• Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencingSanchit Misra, Ankit Agrawal, Wei‐keng Liao — 2011
• CLIP-based prediction of mammalian microRNA binding sitesA. L. Cerdeira, A. W. Cole, Dawn S. Luthe — 2013
• Fuzzy k-mers and their application to comparative genome assemblyJohn Healy — 2013
• Computational analysis of ChIP-seq data.Hongkai Ji — 2010
• New Frontiers of Network Analysis in Systems BiologyAvi Ma’ayan — 2012
• Effects of Single-nucleotide Polymorphisms on microRNA-Based Gene Regulation and Their Association With DiseaseLaurent F. Thomas — 2012
• Algorithms And Tools For Computational Analysis Of Human Transcriptome Using Rna-SeqNan Deng — 2014
• Detection and quantification of alternative splicing variants using RNA-seq.Douglas W. Bryant, Henry D. Priest, Todd C. Mockler — 2012
• Systems support for genomics computing in cloud environmentsTung Nguyen — 2012
• Local assembly and pre-mRNA splicing analyses by high-throughput sequencing dataHsien-Chao Chou — 2012
• Assembly algorithms for next-generation sequence dataAakrosh Ratan — 2009
• Machine learning and high-performance computing: Infrastructure and algorithms for the genome-scale study of genetic and epigenetic regulatory mechanisms with applications in neurosciencePilib Ó Broin — 2014
• Using oligonucleotide signatures to build a system for effective detection of pathogenic bacteria in metagenomic samplesWarren Emmett — 2009
• Grid and high performance computing applied to bioinformaticsManca, Emanuele — 2015
• Bioinformatics challenges of high-throughput SNP discovery and utilization in non-model organismsWayne E. Clarke — 2014

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