gargammel: a sequence simulator for ancient DNA

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 -