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## mapDamage
[](http://bioconda.github.io/recipes/mapdamage2/README.html) [](https://anaconda.org/bioconda/mapdamage2/files)
  [](https://www.repostatus.org/#inactive)
### Installation
mapDamage can be installed via pip:
```bash
pip install mapdamage
```
R and several packages are *post mortem* damage plotting, modeling, and rescaling. Refers to the detailed instructions on the [dedicated page](http://ginolhac.github.io/mapDamage/).
### Introduction
Complete documentation, instructions, examples, screenshots and FAQ are available at [this address](http://ginolhac.github.io/mapDamage/).
[mapDamage2](https://geogenetics.ku.dk/publications/mapdamage2.0/) 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](https://geogenetics.ku.dk/) by the [Orlando Group](https://geogenetics.ku.dk/research_groups/palaeomix_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](http://bioinformatics.oxfordjournals.org/content/early/2013/05/17/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](http://bioinformatics.oxfordjournals.org/content/27/15/2153)
### Test the no-stats part and rescaling
you can test `mapDamage` by running:
```bash
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>
|
