Using tablet for visual exploration of second-generation sequencing data

Briefings in Bioinformatics

Volumn 14, Issue 2, 2013, Pages 193-202

  Milne, Iain ^a   Stephen, Gordon ^a   Bayer, Micha ^a   Cock, Peter J A ^a   Pritchard, Leighton ^a   Cardle, Linda ^a   Shawand, Paul D ^a   Marshall, David ^a  

^a SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

Author keywords

Assembly validation; Second generation sequencing; Visualization

Indexed keywords

ANIMAL; ARTICLE; BIOLOGY; COMPUTER GRAPHICS; COMPUTER PROGRAM; GENETIC DATABASE; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INFORMATION PROCESSING; INTERNET; SEQUENCE ANALYSIS; STATISTICS;

ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; DATA DISPLAY; DATABASES, GENETIC; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTERNET; SEQUENCE ANALYSIS; SOFTWARE;

EID: 84875578097     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbs012     Document Type: Article

References (18)

1. Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics 2010;95: 315-27.
2. Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. JMol Biol 1990;215:403-10.
3. Margulies M, Egholm M, Altman W, etal. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005;437:376-80.
4. Pandey V, Nutter RC, Prediger E. Applied Biosystems SOLiDTM System: ligation-based sequencing. In: Janitz M, (ed). Next Generation Genome Sequencing:Towards Personalized Medicine. Weinheim, Germany: Wiley-VCH, 2008.
5. Milne I, Bayer M, Cardle L, et al. Tablet-next generation sequence assembly visualization. Bioinformatics 2010;26: 401-2.
6. Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009;15: 2078-9.
7. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977; 74:5463-67.
8. Milne I, Lindner D, Bayer M, et al. TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics 2009;25:126-7.
9. Milne I, Shaw P, Stephen G, et al. Flapjack-graphical genotype visualization. Bioinformatics 2010;26:3133-4.
10. Slater GSC, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 2005;6:31.
11. Chevreux B, Wetter T, Suhai S. Genome sequence assembly using trace signals and additional sequence information. Comput Sci Biol: Proc GerConf Bioinformatics 1999;99: 45-56.
12. Camacho C, Coulouris G, Avagyan V, et al. Blast{Thorn}: architecture and applications. BMC Bioinformatics 2009;10:421.
13. Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 2009;19(Suppl. 2):215.
14. Salzberg S, Delcher A, Kasif S, et al. Microbial gene identification using interpolated Markov models. NucleicAcidsRes 1998;26:544-8.
15. Langmead B, Trapnell C, Pop M, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
16. Trapnell C, Pachter L, Salzberg S. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009;25: 1105-1111.
17. Marth GT, Korf I, Yandell MD, et al. A general approach to single-nucleotide polymorphism discovery. Nat Genet 1999; 23:452-6.
18. Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 2010;38:234-6.