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BIOINFORMATICS APPLICATIONS NOTE
Vol. 26 no. 3 2010, pages 401–402
doi:10.1093/bioinformatics/btp666
Sequence analysis
Tablet—next generation sequence assembly visualization
Iain Milne1, Micha Bayer1, Linda Cardle1, Paul Shaw1, Gordon Stephen1, Frank Wright2
and David Marshall1,∗
1Genetics Programme and 2Biomathematics and Statistics Scotland, Scottish Crop Research Institute, Invergowrie,
Dundee, DD2 5DA, UK
Received on September 11, 2009; revised on November 9, 2009; accepted on November 30, 2009
Advance Access publication December 4, 2009
Associate Editor: Joaquin Dopazo
ABSTRACT
Summary: Tablet is a lightweight, high-performance graphical
viewer for next-generation sequence assemblies and alignments.
Supporting a range of input assembly formats, Tablet provides highquality
visualizations showing data in packed or stacked views,
allowing instant access and navigation to any region of interest, and
whole contig overviews and data summaries. Tablet is both multicore
aware and memory efficient, allowing it to handle assemblies
containing millions of reads, even on a 32-bit desktop machine.
Availability: Tablet is freely available for Microsoft Windows, Apple
Mac OS X, Linux and Solaris. Fully bundled installers can be
downloaded from http://bioinf.scri.ac.uk/tablet in 32- and 64-bit
versions.
Contact: tablet@scri.ac.uk
1 INTRODUCTION
The advent of next-generation sequencing (NGS) technologies
such as Roche 454 (Margulies et al., 2005) and Illumina
Solexa (http://www.illumina.com/sequencing) has brought about
a need for fast, efficient and user-friendly tools for analyzing
the outcome of sequencing runs. This includes visualization
software for viewing the resultant assemblies or alignments, for
example, Consed (Gordon et al., 1998), Hawkeye (Schatz et al.,
2007), EagleView (Huang and Marth, 2008), MapView (Bao
et al., 2009), SAMtools’ tview (Li et al., 2009) and Maqview
(http://maq.sourceforge.net/maqview.shtml).
All assembly visualization packages face the following challenges
when dealing with NGS data: processing a very large number of
reads, providing high-quality rendering and navigation of assembled
reads, and supporting a widening range of assembly formats.
Additionally, as analysis and interpretation of the data moves from
large-genome centers to smaller laboratories, there is an increasing
need for biologist-friendly software that has an intuitive user
interface, is available for a range of common desktop platforms
and has no complicated installation dependencies.
With these features in mind, we have developed Tablet, a
lightweight, high-performance and memory efficient assembly
viewer. Tablet is aimed at users of all abilities and combines simple
installation on a desktop machine with ease of use and a visually
rich interface. The application supports both single and multi-core
∗To whom correspondence should be addressed.
processor architectures and will scale its performance according to
the number of processor cores available.
2 FEATURES
Tablet can import data from ACE, AFG, MAQ and SOAP assembly
formats (with preliminary support for SAM), and can handle both
454 and Solexa data. Its visualizations are split into several areas;
the main display provides a view of a single contig at a time, with
reads aligned against their consensus sequence. Reads are colored
according to nucleotide type and subtle use of gradients and color
choice allow visual structure to be maintained even when fully
zoomed out. Tablet will lay out the data in either packed (showing as
many reads per line as possible without overlap) or stacked (showing
one read per line) formats, and allows the user to switch instantly
between them. A sortable list, containing all available contigs shows
contig lengths as well as numbers of reads and annotation features,
and can be dynamically filtered by any of its fields. Continuous
zooming of the entire contig in real time is supported by means of
a slider, and there is also an option for varying the contrast between
variant and non-variant nucleotides which adjusts the brightness
used to display read bases that differ from the consensus, thus aiding
identification of potential single nucleotide polymorphisms (SNPs)
or sequencing errors.
An overview window located above the consensus can display
either a scaled-to-fit summary of all the reads in a contig, or a
coverage graph which shows the read coverage along the entire
length of the contig independent of the current zoom level.
Navigation within a contig is catered for in several ways. First,
the current view point is controlled by manipulating the scroll bars
to move in either direction around the display or by dragging with
the mouse directly on the canvas itself. We also provide a page-ata-time
navigation option that will move the view left or right by the
number of bases that are currently visible. High-speed navigation to
any area of the view is also available by clicking and dragging on
the overview window, which always displays a bounding rectangle
representing the portion of the overall data currently visible within
the main display.
Protein translations are optionally provided for all six reading
frames of the consensus sequence.Annotation features such as SNPs
and indels can either be imported with the assembly file itself or
separately in GFF3 format, and are then listed on a separate tab
attached to the contig list.
© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/2.5) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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I.Milne et al.
Information on a given read is provided as a graphical overlay as
soon as the mouse is moved over it. Tablet will display its name, start
and end positions (optionally with unpadded consensus values), the
sequence length, whether it is complemented or not, and also provide
a scaled-to-fit graphical representation of the bases within the read.
All of the raw data can be copied to the clipboard at any time.
3 IMPLEMENTATION AND PERFORMANCE
Tablet is written in Java and is compatible with any Java-enabled
system with a runtime level of ≥1.6. We provide installable versions
that include everything required to run the application, including
a suitable Java runtime. The installers are available for Windows,
Mac OS X, Linux and Solaris, in both 32- and 64-bit versions. Once
installed and running, Tablet will also monitor our server for new
versions and will prompt, download and update quickly and easily
whenever a new release is available, along with redirecting the user
to a web page describing the new features that have been added.
A prime requisite during development of Tablet has been
computing efficiency and speed. The two main approaches to
handling assembly data in viewers are either memory-based, where
all the data are loaded into memory, or disk-cached, where the data
reside on disk with only the currently visible segment of the dataset
held in memory. Memory-based applications are faster for viewing
and navigation (after an initial delay while loading the data) and can
provide whole dataset overviews and statistical summaries, but the
size of dataset they can handle is limited by the amount of available
memory. In contrast, cache-based applications can display views
from much larger datasets using a minimum of memory, but access
to the data can be orders of magnitude slower (which then affects
navigation and rendering), and the feature sets available are often
limited.
With Tablet, we have chosen a hybrid solution that provides us
with advantages from both approaches. We hold a ‘skeleton’ layout
of the reads in memory, with data on each read limited to just an
internal ID, its position against the consensus or reference sequence
and its length. The nucleotide data itself (efficiently compressed so it
can be read as quickly as possible), along with other supplementary
information—such as the read’s name and its orientation—is held
in an indexed disk-cache and is only accessed (via the read’s ID)
when required. Tablet also allocates memory on a per-contig basis,
including information for features such as how to pack the data
for display, coverage calculations, padded-to-unpadded mappings,
etc. These data are calculated and stored before each contig is
rendered and discarded again after display. This approach allows
us to provide maximum functionality—instant access to any portion
of the data; extremely fast and high-quality rendering; entire dataset
overviews—yet memory usage is kept relatively low.
Comparing data indexing/loading times and memory
consumption across a range of tools for an assembly file
containing ∼2.9 million Illumina Solexa reads of length 51, we
found that the cache-based viewers (Maqview, MapView, tview)
were fairly constant in memory usage (between 35 MB and 70 MB
while viewing), with indexing times varying from 10 s to 50 s,
although memory consumption during indexing did peak as high
as 350 MB with MapView. For the memory-based viewers, we
compared Hawkeye (5500 MB; 107 s), Consed (2600 MB; 73 s) and
Fig. 1. Tablet showing Illumina Solexa reads against an Arabidopsis thaliana
cDNA reference sequence (additional screenshots can be seen online at
http://bioinf.scri.ac.uk/tablet/screenshots.shtml).
EagleView (2450 MB; 98 s). Tablet, being a hybrid, loads the data
in 25 s, and uses just 175 MB of memory.
4 FUTURE WORK
Work is in progress to support paired-end sequence data, and to
enhance Tablet’s visualization of annotation data. We also plan to
further reduce Tablet’s memory requirements by cutting down on
the amount of reference/consensus information held at any time.
Experiments have shown that further reductions should be possible
without compromising data access times, graphical rendering speed
or visualization quality.
ACKNOWLEDGEMENTS
We would like to thank colleagues within the Genetics, Pathology
and BioSS Programmes at SCRI for their input to this project.
Funding: Scottish Government (RERAD, Programme 1); the
Scottish Funding Council and Scottish Enterprise through the
Scottish Bioinformatics Research Network (SBRN) project.
Conflict of Interest: none declared.
REFERENCES
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Huang,W. and Marth,G. (2008) EagleView: a genome assembly viewer for nextgeneration
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Li,H. et al. (2009) The Sequence Alignment/Map format and SAMTools.
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Margulies,M. et al. (2005) Genome sequencing in microfabricated high-density picolitre
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Schatz,M.C. et al. (2007) Hawkeye: an interactive visual analytics tool for genome
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