TY - JOUR
T1 - gargammel
T2 - a sequence simulator for ancient DNA
AU - Renaud, Gabriel
AU - Hanghøj, Kristian Ebbesen
AU - Willerslev, Eske
AU - Orlando, Ludovic Antoine Alexandre
N1 - © The Author 2016. Published by Oxford University Press.
PY - 2017/2/15
Y1 - 2017/2/15
N2 - 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.
AB - 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.
U2 - 10.1093/bioinformatics/btw670
DO - 10.1093/bioinformatics/btw670
M3 - Journal article
C2 - 27794556
SN - 1367-4803
VL - 33
SP - 577
EP - 579
JO - Bioinformatics
JF - Bioinformatics
IS - 4
ER -