bamtk

Description:

BAM-Tk is a software toolkit for dealing with Binary Alignment Map (BAM) files. It allows :

1. abundance matrix construction
2. futures functionalities

Running BAM-Tk

Python libraries

BAM-Tk is designed for Python >=3.6 and requires the following libraries, which will be automatically installed:

• biolib >=0.1.6: common tasks in bioinformatic
• NumPy >=1.9.0: scientific computing with Python.

Third-party software

BAM-Tk makes use of the following 3rd party dependencies and assumes they are on your system path:

• samtools >= 0.1.19: Li H., et al. 2009 The Sequence alignment/map (SAM) format and SAMtools Bioinformatics, 25, 2078-9.

Please cite these tools if you use BAM-Tk in your work.

Installation

Once the third-party dependencies have been installed, BAM-Tk can be installed using pip:

python -m pip install git+https://github.com/meb-team/BAM-Tk.git

Need help ?

1. Access the help menu (bamtk -h)
2. Run an example (bamtk mm_features tests/data/toy.fa.fai tests/bamlist.txt tests/results)

Bugs

• Submit problems or requests here: https://github.com/meb-team/BAM-Tk/issues/

Citation

Written by Corentin Hochart (corentin.hochart@uca.fr), UMR CNRSS 6023 Laboratoire Genome et Environement (LMGE) as part of the ANR Eureka project. Released under the terms of the GNU General Public License v3. bamtk version v0.1.1.