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Quality control tools for NGS alignment file

Project description

.. image::
:width: 200 px
:alt: generated at
:align: right


Version 0.6.5

`Github Page <>`_

`Pypi Page <>`_

`MHammell Lab <>`_

Installation guide for BAMQC for from source installs

`Source Code <>`_

`Pypi <>`_

* `python2.7 <>`_
* `R <>`_
* `corrplot <>`_
* `GCC 4.8.1 or greater <>`_

While there are multiple methods of installing the prerequistes it may
help to look at (if using a yum based linux distro):

* `Devtoolset-3 <>`_ for GCC compilers
* `IUS <>`_ for Python2.7
* `Software Collections <>`_ for collections of software (like devtoolset 3 or python)
* `rpmfinder <>`_ for searching rpms across mutliple systems


make sure that the GCC comiler is in your PATH

.. code:: bash
export PATH=/path/to/gcc:$PATH

make sure that python2.7 is is in your PYTHONPATH, for permance add it to your .bashrc

.. code:: bash
export PYTHONPATH=/path/to/python2.7/site-packages:$PYTHONPATH

There are three methods of installation of BAMqc, from source,, and from pypi, once prequistes are setup.

*From Source*

download source

.. code:: bash
tar xvfz bamqc-0.6.4.tar.gz
cd bamqc-0.6.4

run make on htslib

note: make sure to have -fPIC in your cflags ie: ``export CFLAGS="$CFLAGS -fPIC"``

.. code:: bash

cd src/htslib

run make

.. code:: bash

cd ../..


.. code:: bash

python2.7 install

*From Pypi*

.. code:: bash

pip2.7 install BAMqc


Ying Jin:

Acknowledgements goes to

#) Samtools and pysam contributors
#) Molly Hammell and members of her laboratory at Cold Spring Harbor Laboratory
#) Users' valuable feedback

Copying & distribution

BAMQC is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but *WITHOUT ANY WARRANTY*; without even the implied warranty of
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with BAMQC. If not, see `this website <>`_.

Project details

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