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Manual Reference Pages  - MAQVIEW (1)

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Maqview - Maq alignment indexer and viewer

CONTENTS

Synopsis
Description
License
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Authors

maqindex in.map [ref_id [start end]]

maqview in.map

Maqview is a set of programs that achieves fast random access to the alignment file generated by ‘maq map’, and displays the alignment with a nice GUI (Graphical User Interface). It is highly efficient in speed, memory and disk usage. Maqview is based on OpenGL and is known to work on both Mac OS X and Linux. Porting to Windows is in principle easy.

maqindex [-l level] in.map [ref_id [begin end]]

Program map_index indexes a maq alignment file in.map and quickly retrieves all the reads is a specified region. If ref_id is not specified, maqindex will index in.map and generate indexes on the disk; otherwise, maqview will retrieve alignments in maq’s mapview format. Argument ref_id is an interger representing the index order of reference sequences stored in in.map.

Indexing is required for using maqview.

maqview in.map

Program maqview displays the read alignment in a graphical window. It has two views: sequence view and box view. In the sequence view, read sequences will be printed on the screen. Darker bases indicate lower base qualities and red ones show the differences in comparison to the majority-rule consensus (not the maq consensus). In the box view, different types of nucleotides are represented as colour boxes with green for A, cyan for C, orange for G, red for T and dark gray for N. The saturation of colours indicates the base qualities and the thickness lines of reads shows the mapping qualities of read alignments. Zooming in/out is supported only in the box view. In both views, the status bar at the bottom of the window will show some information about the key touches, and read names and base qualities pointed by the mouse.

Navigating the alignment is accomplished by vaious key bindings.

o	Key bindings: ? Display help <F1> Sequence view <F2> Box view p Switch to the previous reference sequence n Switch to the next reference sequence r Refresh h / <Left> Move left by one base l / <Right> Move right by one base k / <Up> Move up by one line j / <Down> Move down by one line > Move to the next read < Move to the previous read g / <Home> Move to the begining of the current reference G / <End> Move to the end of the current reference u / <PageUp> Move left by one page <Space>/<PageDn> Move right by one page Hold <Shift> Move by 100 bases Hold <Ctrl> Move by 1000 bases <Enter> Toggle on/off right auto-scrolling ^b Toggle on/off left auto-scrolling + Zoom in - Zoom out 0 Zoom to the default scale q Toggle show/hide mapping qualities e Toggle display SE/PE mapping qualities o Open a new alignment file <Esc> Exit
o	Enter an integer and then press <Enter> to jump to the required position.
o	Enter an integer and then press a key other than <Enter> to speed up scrolling by the specified factor.
o	Left click and drag the yellow cross in the square to move along the sequence. Right click the reference to highlight a column.

GNU General Public License (GPL)

<http://maq.sourceforge.net>

Jue Ruan <ruanjue@genomics.org.cn> for writing and maintaining the whole software.

Heng Li <lh3@sanger.ac.uk> for testing the program and drafting the documentations.

Mengyao Zhao <zhaomengyao@gmail.com> for designing the color schemes.