gargammel: a sequence simulator for ancient DNA
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gargammel : a sequence simulator for ancient DNA. / Renaud, Gabriel; Hanghøj, Kristian Ebbesen; Willerslev, Eske; Orlando, Ludovic Antoine Alexandre.
In: Bioinformatics, Vol. 33, No. 4, 2017, p. 577-579.Research output: Contribution to journal › Journal article › Research › peer-review
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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
Y1 - 2017
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.AVAILABILITY AND IMPLEMENTATION: The package is publicly available on github: https://grenaud.github.io/gargammel/ and released under the GPL.CONTACT: gabriel.renaud@snm.ku.dkSupplementary information: Supplementary data are available at Bioinformatics online.
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.AVAILABILITY AND IMPLEMENTATION: The package is publicly available on github: https://grenaud.github.io/gargammel/ and released under the GPL.CONTACT: gabriel.renaud@snm.ku.dkSupplementary information: Supplementary data are available at Bioinformatics online.
U2 - 10.1093/bioinformatics/btw670
DO - 10.1093/bioinformatics/btw670
M3 - Journal article
C2 - 27794556
VL - 33
SP - 577
EP - 579
JO - Computer Applications in the Biosciences
JF - Computer Applications in the Biosciences
SN - 1471-2105
IS - 4
ER -
ID: 172510576