title: gargammel: a sequence simulator for ancient DNA.
abstract: Ancient DNA has emerged as a remarkable tool to infer the history of extinct species and past populations. However, many of its characteristics, such as extensive fragmentation, damage and contamination, can influence downstream analyses. To help investigators measure how these could impact their analyses in silico , we have developed gargammel, a package that simulates ancient DNA fragments given a set of known reference genomes. Our package simulates the entire molecular process from post-mortem DNA fragmentation and DNA damage to experimental sequencing errors, and reproduces most common bias observed in ancient DNA datasets.
  
  
  
  The package is publicly available on github: https://grenaud.github.io/gargammel/ and released under the GPL.
  
  
  
  gabriel.renaud@snm.ku.dk.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark.
authors: Gabriel
authors: G
authors: Renaud
authors: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark.|Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, Toulouse, France.
authors: Kristian
authors: K
authors: Hanghøj
authors: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark.|Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK.|Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors: Eske
authors: E
authors: Willerslev
authors: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark.|Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, Toulouse, France.
authors: Ludovic
authors: L
authors: Orlando
mesh_terms: D000818:Animals; D003198:Computer Simulation; D059018:DNA Contamination; D004249:DNA Damage; D000072441:DNA, Ancient / Q000737:chemistry*; D006801:Humans; D011180:Postmortem Changes; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
chemical_list: D000072441:DNA, Ancient