friedpine / mapdamage

mapDamage: tracking and quantifying damage patterns in ancient DNA sequences

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 .

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.