mapDamage: testing for damage patterns in ancient DNA sequences – University of Copenhagen

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Documentation for published script in Bioinformatics

Link to the most recent version (25. April 2013): mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.

mapDamage: testing for damage patterns in ancient DNA sequences

Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L. Bioinformatics. 2011 27(15):2153-5

News May 2012

Development version for mapDamage is now hosted on github at the following address: https://github.com/ginolhac/mapDamage

If you find any bugs, please try the current version 0.3.6 and feel free to report if it's still not fixed.

Newest version (April 2012)

Go to Github for new version

Version 0.3.3. pl (January 2012)

Main file

mapDamage 0.3.3.html (6 kb)

Perl script

mapDamage 0.3.3.pl (63 kb)

Version 0.3.2. (December 2011)

Main file

mapDamage 0.3.2.html

Perl script

mapDamage 0.3.2.pl

Original version (June 2011)

Main file

mapDamage.html

And the original Perl script

mapDamage-0.2.pl (52 kB)

Examples with real datasets

Datasets:

Saqqaq_12W_Phusion_6_3h-q25.sam.gz (41.2 MB)

Saqqaq_12X_HiFi_3h-q25.sam.gz (43.4 MB)

Map results:

results_Saqqaq_12W_Phusion_6_3h-q25.sam.filtered.tar.gz (18.4 MB)

results_Saqqaq_12X_HiFi_3h-q25.sam.filtered.tar.gz (18.8 MB)

Plot results:

FragMisincorporationHiFi.jpg

FragMisincorporationHiFi.jpg (96 kB)

FragMisincorporationHiFi.pdf (0.8 MB)

FragMisincorporationPhusion.pdf (0.8 MB)

Examples with simulated datasets

Datasets:

Prufer2010_6Nsim.tar.bz2

Plot results:

FragMisincorporationNSim1F.pdf (0.8 MB)

FragMisincorporationNSim2F.pdf (0.8 MB)

FragMisincorporationNSim3F.pdf (0.8 MB)

FragMisincorporationNSim4F.pdf (0.8 MB)

FragMisincorporationNSim5F.pdf (0.8 MB)

FragMisincorporationNSim6F.pdf (0.8 MB)

Further info:

Contact Aurelien Ginolhac