mapDamage: tracking and quantifying damage patterns in ancient DNA sequences
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bin The --mapdamage-modules option can now be specified with an equal sign Feb 19, 2015
mapdamage Add explicit check for empty FASTA/fai files. Jul 30, 2018
.gitignore Updated the ignore file to incorporate various temporary files Sep 3, 2013
LICENSE.txt
MANIFEST python version first commit Nov 12, 2012
MANIFEST.in add reading a BAM from stdin Nov 14, 2012
README.md update README Aug 2, 2016
setup.py Improve tag handling. Apr 27, 2017

README.md

Important

Users with versions dating prior to June 12 2013 please update. A nasty bug that caused the statistical part of mapDamage to use half of the data for estimation of the damage parameters, sorry for the inconvenience.

Introduction

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

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

Mapdamage is developed at the Centre for GeoGenetics by the Orlando Group .

Web interface

Anna Kostikova from insideDNA implemented a web interface for mapDamage.
Users can adjust the cloud ressources in terms of RAM/CPU to perform their analysis. She wrote a tutorial explaining how to use this web interface (sign up required)

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 is described 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

Contact

Please report bugs and suggest possible improvements to Aurélien Ginolhac, Mikkel Schubert or Hákon Jónsson by email: aginolhac at snm.ku.dk, MSchubert at snm.ku.dk or jonsson.hakon at gmail.com.