mapdamage 2.2.3

mapDamage

Installation

mapDamage can be installed via pip:

pip install mapdamage

R and several packages are post mortem damage plotting, modeling, and rescaling. Refers to the detailed instructions on the dedicated page.

Introduction

Complete documentation, instructions, examples, screenshots and FAQ are available at this address.

mapDamage2 is a computational framework written in Python3 and R, which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

mapDamage was developed at the Centre for GeoGenetics by the Orlando Group.

Citation

If you use this program, please cite the following publication: Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 23rd April 2013. doi: 10.1093/bioinformatics/btt193

The original mapDamage1 was published in the following article: Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics 2011 27(15):2153-5 http://bioinformatics.oxfordjournals.org/content/27/15/2153

Test the no-stats part and rescaling

you can test mapDamage by running:

cd mapDamage/mapdamage/
python3 mp_test.py

should return

Started with the command: /usr/local/bin/mapDamage -i tests/test.bam -r tests/fake1.fasta -d tests/results --no-stats
 Reading from 'tests/test.bam'
 Writing results to 'tests/results/'
pdf tests/results/Fragmisincorporation_plot.pdf generated
additional tests/results/Length_plot.pdf generated
Successful run
.
----------------------------------------------------------------------
Ran 2 tests in 3.357s

OK

Contact

Please report bugs and suggest possible improvements on GitHub: https://github.com/ginolhac/mapDamage/issues/new