Advertisement

Tablet: Visualizing Next-Generation Sequence Assemblies and Mappings

  • Iain MilneEmail author
  • Micha Bayer
  • Gordon Stephen
  • Linda Cardle
  • David Marshall
Part of the Methods in Molecular Biology book series (MIMB, volume 1374)

Abstract

This chapter is designed to be a practical guide to using Tablet for the visualization of next/second-generation (NGS) sequencing data. NGS data is being produced more frequently and in greater data volumes every year. As such, it is increasingly important to have tools which enable biologists and bioinformaticians to understand and gain key insights into their data. Visualization can play a key role in the exploration of such data as well as aid in the visual validation of sequence assemblies and features such as single nucleotide polymorphisms (SNPs). We aim to show several use cases which demonstrate Tablet’s ability to visually highlight various situations of interest which can arise in NGS data.

Key words

Visualization Mapping Assembly Next-generation sequencing SNPdiscovery 

References

  1. 1.
    Milne I, Stephen G, Bayer M et al (2013) Using tablet for visual exploration of second-generation sequencing data. Brief Bioinform 14(2):193–202CrossRefPubMedGoogle Scholar
  2. 2.
    Milne I, Bayer M, Cardle L et al (2010) Tablet—next generation sequence assembly visualization. Bioinformatics 26(3):401–402PubMedCentralCrossRefPubMedGoogle Scholar
  3. 3.
    Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25:2078–2079PubMedCentralCrossRefPubMedGoogle Scholar
  4. 4.
    Comadran J, Kilian B, Russell J et al (2012) Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nat Genet 44:1388–1392CrossRefPubMedGoogle Scholar
  5. 5.
    Close TJ, Bhat RR, Lonardi S (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582PubMedCentralCrossRefPubMedGoogle Scholar
  6. 6.
    Nakamura K, Oshima T, Morimoto T et al (2011) Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res. doi: 10.1093/nar/gkr344 Google Scholar
  7. 7.
    Meacham F, Boffelli D, Dhahbi J et al (2011) Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics 12:451PubMedCentralCrossRefPubMedGoogle Scholar
  8. 8.
    Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63PubMedCentralCrossRefPubMedGoogle Scholar
  9. 9.
    Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. doi: 10.1093/bioinformatics/btp120 PubMedCentralPubMedGoogle Scholar
  10. 10.
    Stanke M, Waack S (2003) Gene prediction with a Hidden-Markov Model and a new intron submodel. Bioinformatics 19(2):215–225Google Scholar
  11. 11.
    The International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711–716Google Scholar
  12. 12.
    Liu H, Bayer M, Druka A et al (2014) An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley. BMC Genomics 15:104PubMedCentralCrossRefPubMedGoogle Scholar
  13. 13.
    Kumar S, Banks TW, Cloutier S (2012) SNP discovery through next-generation sequencing and Its applications. Int J Plant Genomics. doi: 10.1155/2012/831460 Google Scholar
  14. 14.
    Nielsen R, Paul JS, Albrechtsen A et al (2011) Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12:443–451PubMedCentralCrossRefPubMedGoogle Scholar
  15. 15.
    Pabinger S, Dander A, Fischer M et al (2014) A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform 15(2):256–278PubMedCentralCrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Iain Milne
    • 1
    Email author
  • Micha Bayer
    • 1
  • Gordon Stephen
    • 1
  • Linda Cardle
    • 1
  • David Marshall
    • 1
  1. 1.Information and Computational Sciences, The James Hutton InstituteInvergowrie, DundeeUK

Personalised recommendations