SAMSCOPE: An opengl-based real-time interactive scale-free SAM viewer

Kris Popendorf, Yasubumi Sakakibara

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Existing SAM visualization tools like 'samtools tview' (Li et al., 2009) are limited to a small region of the genome, and tools like Tablet (Milne et al., 2010) are limited to a relatively small number of reads and may fail outright on large datasets. We need to visualize complex ChIP-Seq and RNA-Seq features such as polarity as well as coverage across whole 3 Gbp genomes such as Human. We have addressed these problems in a lightweight visualization system called SAMSCOPE accelerated by OpenGL. The extensive pre-processing and fast OpenGL interface of SAMSCOPE provides instantaneous and intuitive browsing of complex data at all levels of detail across multiple experiments.

Original languageEnglish
Article numberbts122
Pages (from-to)1276-1277
Number of pages2
JournalBioinformatics
Volume28
Issue number9
DOIs
Publication statusPublished - 2012 May

Fingerprint

OpenGL
Genome
Visualization
Genes
Real-time
Polarity
Browsing
RNA
Large Data Sets
Tablets
Instantaneous
Preprocessing
Intuitive
Coverage
Chip
Processing
Experiment
Experiments
Human
Datasets

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

SAMSCOPE : An opengl-based real-time interactive scale-free SAM viewer. / Popendorf, Kris; Sakakibara, Yasubumi.

In: Bioinformatics, Vol. 28, No. 9, bts122, 05.2012, p. 1276-1277.

Research output: Contribution to journalArticle

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