MAQVIEW(1)

📦
version 0.2.5 · 4 versions
, in debian bookworm, ubuntu noble

🌸 MAQVIEW(1) — Bioinformatics Tools 💅

okay bestie, sit down, hydrate, and let me tell you about Maqview — the maq alignment indexer and viewer. ✨

✨ NAME ✨

Maqview — Maq alignment indexer and viewer 🦋

🎀 SYNOPSIS 🎀

maqindex -i|-v|-b [-c in.cns] in.map [chr[:start[-end]] [...]]

maqview [-c in.cns] in.map

👑 DESCRIPTION 👑

So Maqview is actually a set of programs, not one little guy. Together they do two things: get fast random access to the alignment file that maq map generates, and then display that alignment in a nice GUI (that's Graphical User Interface, for the uninitiated 💖). It's highly efficient in speed, memory, and disk usage — the whole trifecta, no cap. Maqview is built on OpenGL and is known to work on both Mac OS X and Linux. Porting it to Windows is, in principle, easy. 👑

🧚 maqindex 🧚

maqindex -i|-v|-b [-c in.cns] in.map [chr[:start[-end]] [...]]
  • -i — Index the alignment file 📇
  • -v — Print the alignment in the specified region in the maq mapview format 🖨️
  • -b — Dump the alignment in the specified region in the binary .map format 💾
  • -c FILE — Index the Maq consensus file for viewing in maqview at the same time 🫶

The program maqindex either indexes a maq alignment file in.map or quickly retrieves all the reads in one or multiple regions. You must use one of -i, -v and -b — pick one, bestie, it's not optional. For -v or -b, you have to specify at least one region, like chrX, chrX:1000 or chrX:1,000-2,000. Multiple regions are allowed, so go off. 🌈

💜 maqview 💜

maqview [-c in.cns] in.map
  • -c FILE — The Maq consensus file 🍓

The program maqview displays the read alignment in a graphical window. When in.cns is specified, the top sequence is the reference, followed by the Maq consensus sequence; otherwise, the majority-rule consensus will be calculated. 🧮

Maqview 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 reference if in.cns is specified — or to the majority-rule consensus if it isn't. In the box view, different types of nucleotides are represented as colour boxes: green for A, cyan for C, orange for G, red for T and dark gray for N. The saturation of the colours indicates the base qualities, and the thickness of the lines of reads shows the mapping qualities of the read alignments. Zooming in/out is supported only in the box view, so don't go looking for it in sequence view, ok? 👀 In both views, the status bar at the bottom of the window will show some information about the key touches, plus read names and base qualities pointed at by the mouse. 🖱️

Navigating the alignment is accomplished by various key bindings. 💅

  • Key bindings:
    • ? — Display help 🙋
    • <Esc> — Exit 🚪
    • <F1> — Sequence view 🧬
    • <F2> — Box view 🎁
    • p — Switch to the previous reference sequence ⏪
    • n — Switch to the next reference sequence ⏩
    • r — Refresh 🔄
    • <digits> <Enter> — Move to the position pointed by <digits> 🔢
    • 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 beginning 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 📄
    • <Shift> <Arrow> — Move by 100 bases 💯
    • <Ctrl> <Arrow> — Move by 1000 bases 🔥
    • <Ctrl> + — Add a new view ➕
    • <Ctrl> - — Remove the current view ➖
    • <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 📂
  • Enter an integer and then press <Enter> to jump to the required position. 🎯
  • Enter an integer and then press a key other than <Enter> to speed up scrolling by the specified factor. 🚀
  • Left click and drag the yellow cross in the square to move along the sequence. Right click the reference to highlight a column. 🟨

🫶 LICENSE 🫶

GNU General Public License (GPL) — the good stuff. 📜

🌐 AVAILABILITY 🌐

<http://maq.sourceforge.net>

💖 AUTHORS 💖

  • Jue Ruan <ruanjue@genomics.org.cn> — for writing and maintaining the whole software. the GOAT, honestly 👑
  • Heng Li <lh3@sanger.ac.uk> — for testing the program and drafting the documentations. 📝
  • Mengyao Zhao <zhaomengyao@gmail.com> — for designing the color schemes. 🎨

and that's the whole page bestie, tysm for reading 🥹 this was maqview-0.2.4, dated 2022-11-29, from the MAQVIEW(1) manual — periodt. 💅✨🦋

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