De-multiplex NGS reads using trie data structures. It's fast, and made of tries!
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. Early results indicate far improved accuracy and speed over existing de-multiplexers. Unscientific trials show AXE processes more than 500,000 reads per second.
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 https://axe-demultiplexer.readthedocs.org/en/latest/, along with full documentation and a basic description of the algorithm.
For arcane reasons, the name of the
axe binary changed to
with version 0.3.0. Apologies for the inconvenience, this was required to
axe installable in Debian and its derivatives. Command-line usage
did not change.
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
cmake -DCMAKE_INSTALL_PREFIX=/path/to/your/prefix ..
cmake -DCMAKE_INSTALL_PREFIX=$HOME ..
For me, using
~/ as the prefix will install
GNU/Linux, and (if I had one)
/Users/kevin/bin on Mac OSX.It's also wise to
make install not
sudo make install when installing to a home directory.
- cmake. This is installable via
sudo apt-get install cmakeon Debian based systems, or
brew install cmakeusing homebrew on OS X.
- zlib version >= 1.2.5. On Debian, use the package
- libqes, tinytest, libgsl and libdatrie (bundled in source, if you used
git clone --recursiveor an installation tarball. Otherwise, run
git submodule update --init).
You'll possibly need to install zlib to your chosen prefix (e.g.
supercomputers, which often have very old versions of zlib. To do so:
wget http://zlib.net/zlib-1.2.8.tar.gz tar xvf zlib-1.2.8.tar.gz cd zlib-1.2.8 ./configure --prefix=<your_prefix> # e.g. --prefix=$HOME make && make install
And then, use the following cmake command, assuming your prefix is
cmake -DCMAKE_INSTALL_PREFIX=$HOME -DZLIB_ROOT=$HOME ..
We have a preprint describing AXE up at http://www.biorxiv.org/content/early/2017/07/07/160606
We use Semantic Versioning. See semver.org
The source of axe itself, namely
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
The source of
tinytest, located in
tests/tinytest, is Copyright 2009-2012
tinytest is distributed under the 3-clause BSD license.
tinytest is hosted at Nick's github page.
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
libdatrie is hosted at Theppitak Karoonboonyanan's