BAMQC 0.6.4

Quality control tools for NGS alignment file

Version 0.6.4

Github Page

MHammell Lab

Installation guide for BAMQC for from source installs

Source Code

Prerequisites:

• 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

Setup

make sure that the GCC comiler is in your PATH

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

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

From Source

download source

run make on htslib

run make

From Setup.py

Contacts

Ying Jin: [e-mail]

Acknowledgements goes to

1. Samtools and pysam contributors

2. Molly Hammell and members of her laboratory at Cold Spring Harbor Laboratory

3. 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 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 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.