Using Tablet for visual exploration of second-generation sequencing data

Using Tablet for visual exploration of second-generation sequencing data

24 March 2012 | Iain Milne, Gordon Stephen, Micha Bayer, Peter J.A. Cock, Leighton Pritchard, Linda Cardle, Paul D. Shaw and David Marshall
The article discusses the use of Tablet, a high-performance graphical viewer for visualizing second-generation sequencing (2GS) data. Tablet is designed to handle the challenges posed by 2GS technologies, including large data volumes, short read lengths, and diverse data formats. It provides features such as whole-reference coverage overviews, variant highlighting, paired-end read mark-up, GFF3-based feature tracks, and protein translations, which are essential for quality assurance and scientific discovery. The software supports a wide range of file formats, including ACE, AFG, MAQ, SOAP, SAM, and BAM, and can be installed on various operating systems. Tablet is lightweight, efficient, and allows users to view and analyze data interactively. It supports both 2GS and Sanger data, and includes features such as zooming, panning, and real-time highlighting of variant bases. The software also enables the export of read data in FASTA format and provides tools for annotation and visualization of gene models. Tablet is useful for visual inspection of transcripts from de novo RNA sequence assemblies and for variant detection and validation. It supports a hybrid viewer approach, combining memory-based and disk-based strategies for efficient data handling. The software is written in Java and is freely available for download. Future developments include enhancing visualization features, supporting hierarchical data structures, and improving search functionality. Tablet is an essential tool for analyzing 2GS data, providing a rich and responsive graphical environment for researchers.The article discusses the use of Tablet, a high-performance graphical viewer for visualizing second-generation sequencing (2GS) data. Tablet is designed to handle the challenges posed by 2GS technologies, including large data volumes, short read lengths, and diverse data formats. It provides features such as whole-reference coverage overviews, variant highlighting, paired-end read mark-up, GFF3-based feature tracks, and protein translations, which are essential for quality assurance and scientific discovery. The software supports a wide range of file formats, including ACE, AFG, MAQ, SOAP, SAM, and BAM, and can be installed on various operating systems. Tablet is lightweight, efficient, and allows users to view and analyze data interactively. It supports both 2GS and Sanger data, and includes features such as zooming, panning, and real-time highlighting of variant bases. The software also enables the export of read data in FASTA format and provides tools for annotation and visualization of gene models. Tablet is useful for visual inspection of transcripts from de novo RNA sequence assemblies and for variant detection and validation. It supports a hybrid viewer approach, combining memory-based and disk-based strategies for efficient data handling. The software is written in Java and is freely available for download. Future developments include enhancing visualization features, supporting hierarchical data structures, and improving search functionality. Tablet is an essential tool for analyzing 2GS data, providing a rich and responsive graphical environment for researchers.
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