https://github.com/kdm9/axe

Rapid competitive read demulitplexer. Made with tries.
https://github.com/kdm9/axe

Last synced: 5 months ago
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Rapid competitive read demulitplexer. Made with tries.

• Host: GitHub
• URL: https://github.com/kdm9/axe
• Owner: kdm9
• License: gpl-3.0
• Created: 2014-06-01T05:55:02.000Z (about 11 years ago)
• Default Branch: master
• Last Pushed: 2023-10-21T13:02:15.000Z (over 1 year ago)
• Last Synced: 2024-12-29T15:10:58.823Z (5 months ago)
• Language: C
• Homepage: http://axe-demultiplexer.rtfd.io
• Size: 1.09 MB
• Stars: 23
• Watchers: 4
• Forks: 5
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

        
AXE

===

> De-multiplex NGS reads using trie data structures. It's fast, and made of tries!

[![DOI](https://zenodo.org/badge/6357/kdmurray91/axe.svg)](https://zenodo.org/badge/latestdoi/6357/kdmurray91/axe)

[![Documentation Status](https://readthedocs.org/projects/axe-demultiplexer/badge/?version=latest)](https://readthedocs.org/projects/axe-demultiplexer/?badge=latest)

[![Join the chat at https://gitter.im/axe-demultipexer/Lobby](https://badges.gitter.im/axe-demultipexer/Lobby.svg)](https://gitter.im/axe-demultipexer/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)

AXE very rapidly selects the optimal index present in a sequence read, even

in the presence of sequencing errors. The algorithm is able to handle

combinatorial indexing, indexes of differing length, and several mismatches

per index. Benchmarking results indicate far improved accuracy and speed over

existing de-multiplexers. Unscientific trials show AXE processes more than

500,000 reads per second.

Quick Start

-----------

### `conda`

[![](https://img.shields.io/badge/Anaconda.org-0.3.3-blue.svg?style=flat-square)](https://anaconda.org/kdm801/axe-demultiplexer/)

```

mamba install -c kdm801 axe-demultiplexer

```

### From source

To install on UNIX-like systems (Mac, Linux), get the dependencies (zlib and cmake, see below), and:

    git clone --recursive https://github.com/kdmurray91/axe.git axe

    cd axe

    cmake .

    sudo make install

A tutorial on the usage of Axe is available at , along with full documentation and a basic description of the algorithm.

Important Note

--------------

**For arcane reasons, the name of the ``axe`` binary changed to ``axe-demux``

with version 0.3.0. Apologies for the inconvenience, this was required to

make ``axe`` installable in Debian and its derivatives. Command-line usage

did not change.**

Installation:

-------------

Currently, only recent GNU/Linux systems are officially supported. All code and

the build system is portable, so compilation and use on other systems should be

possible, I just don't have machines available to test. Please report any

installation issues on any system as GitHub bugs and I'll do my best to sort

them out.

To install to a prefix, as you would with `./configure --prefix` with the

autotools build system, please use the following cmake command in place of the

one above:

    cmake -DCMAKE_INSTALL_PREFIX=/path/to/your/prefix ..

e.g.:

    cmake -DCMAKE_INSTALL_PREFIX=$HOME ..

For me, using `~/` as the prefix will install `axe` under `/home/kevin/bin` on

GNU/Linux, and (if I had one) `/Users/kevin/bin` on Mac OSX.It's also wise to

use `make install` not `sudo make install` when installing to a home directory.

### Dependencies:

- cmake. This is installable via `sudo apt-get install cmake` on Debian based

  systems, or `brew install cmake` using homebrew on OS X.

- zlib version >= 1.2.5. On Debian, use the package `zlib1g-dev`.

- libqes, tinytest, libgsl and libdatrie (bundled in source, if you used

  `git clone --recursive` or an installation tarball. Otherwise, run

  `git submodule update --init`).

You'll possibly need to install zlib to your chosen prefix (e.g. `~/`) on

supercomputers, which often have very old versions of zlib. To do so:

    wget http://zlib.net/zlib-1.2.8.tar.gz

    tar xvf zlib-1.2.8.tar.gz

    cd zlib-1.2.8

    ./configure --prefix= # e.g. --prefix=$HOME

    make && make install

And then, use the following cmake command, assuming your prefix is `~/`:

    cmake -DCMAKE_INSTALL_PREFIX=$HOME -DZLIB_ROOT=$HOME ..

Publication

-----------

We have a paper describing AXE published in Bioinformatics https://academic.oup.com/bioinformatics/article/34/22/3924/5026649

A [PDF is available](https://raw.githubusercontent.com/kdm9/axe-paper/master/oxford-final/axe-formatted.pdf?token=GHSAT0AAAAAABVH27O27FSFX47CB5FAUFZ6YV5NNQA)

Versioning

----------

We use Semantic Versioning. See [semver.org](http://semver.org)

LICENSE

-------

The source of axe itself, namely `src/axe*.[ch]` and `tests/*.[ch]`, is

Copyright 2014-2015 Kevin Murray. All axe source code is licensed under the GNU

GPL version 3 or greater, a copy of which is included with this source as

`LICENCE.txt`

The source of `tinytest`, located in `tests/tinytest`, is Copyright 2009-2012

Nick Matthewson; `tinytest` is distributed under the 3-clause BSD license.

`tinytest` is hosted at [Nick's github page](https://github.com/nmathewson/tinytest).

The source of `libgsl`, located in `src/gsl`, is Copyright (C) 1996, 1997,

1998, 1999, 2000, 2007 Gerard Jungman and Brian Gough. It is licensed under the

GNU General Public License, vesion 3 or greater.

The source of `libdatrie`, located in `src/datrie`, is Copyright 2006 Theppitak

Karoonboonyanan, and is licensed under the GNU LGPL version 2.1 per

`src/datrie/COPYING`. `libdatrie` is hosted at Theppitak Karoonboonyanan's

website, [here](http://linux.thai.net/~thep/datrie/datrie.html).