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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 journalJournal articleResearchpeer-review

Harvard

Renaud, G, Hanghøj, KE, Willerslev, E & Orlando, LAA 2017, 'gargammel: a sequence simulator for ancient DNA', Bioinformatics, vol. 33, no. 4, pp. 577-579. https://doi.org/10.1093/bioinformatics/btw670

APA

Renaud, G., Hanghøj, K. E., Willerslev, E., & Orlando, L. A. A. (2017). gargammel: a sequence simulator for ancient DNA. Bioinformatics, 33(4), 577-579. https://doi.org/10.1093/bioinformatics/btw670

Vancouver

Renaud G, Hanghøj KE, Willerslev E, Orlando LAA. gargammel: a sequence simulator for ancient DNA. Bioinformatics. 2017;33(4):577-579. https://doi.org/10.1093/bioinformatics/btw670

Author

Renaud, Gabriel ; Hanghøj, Kristian Ebbesen ; Willerslev, Eske ; Orlando, Ludovic Antoine Alexandre. / gargammel : a sequence simulator for ancient DNA. In: Bioinformatics. 2017 ; Vol. 33, No. 4. pp. 577-579.

Bibtex

@article{3850e86e14444c07b4e4f0d1180d2abc,
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.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.",
author = "Gabriel Renaud and Hangh{\o}j, {Kristian Ebbesen} and Eske Willerslev and Orlando, {Ludovic Antoine Alexandre}",
note = "{\circledC} The Author 2016. Published by Oxford University Press.",
year = "2017",
doi = "10.1093/bioinformatics/btw670",
language = "English",
volume = "33",
pages = "577--579",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "4",

}

RIS

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

VL - 33

SP - 577

EP - 579

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 4

ER -

ID: 172510576