EAGER: efficient ancient genome reconstruction

BACKGROUND: The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. RESULTS: Here we introduce EAGER, a time-efficient pipeline, which greatly simplifies the analysis of large-scale genomic data sets. EAGER provides features to preprocess, map, authenti...

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Autores principales: Peltzer, Alexander, Jäger, Günter, Herbig, Alexander, Seitz, Alexander, Kniep, Christian, Krause, Johannes, Nieselt, Kay
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815194/
https://www.ncbi.nlm.nih.gov/pubmed/27036623
http://dx.doi.org/10.1186/s13059-016-0918-z
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author Peltzer, Alexander
Jäger, Günter
Herbig, Alexander
Seitz, Alexander
Kniep, Christian
Krause, Johannes
Nieselt, Kay
author_facet Peltzer, Alexander
Jäger, Günter
Herbig, Alexander
Seitz, Alexander
Kniep, Christian
Krause, Johannes
Nieselt, Kay
author_sort Peltzer, Alexander
collection PubMed
description BACKGROUND: The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. RESULTS: Here we introduce EAGER, a time-efficient pipeline, which greatly simplifies the analysis of large-scale genomic data sets. EAGER provides features to preprocess, map, authenticate, and assess the quality of ancient DNA samples. Additionally, EAGER comprises tools to genotype samples to discover, filter, and analyze variants. CONCLUSIONS: EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-0918-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-48151942016-04-01 EAGER: efficient ancient genome reconstruction Peltzer, Alexander Jäger, Günter Herbig, Alexander Seitz, Alexander Kniep, Christian Krause, Johannes Nieselt, Kay Genome Biol Software BACKGROUND: The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. RESULTS: Here we introduce EAGER, a time-efficient pipeline, which greatly simplifies the analysis of large-scale genomic data sets. EAGER provides features to preprocess, map, authenticate, and assess the quality of ancient DNA samples. Additionally, EAGER comprises tools to genotype samples to discover, filter, and analyze variants. CONCLUSIONS: EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-0918-z) contains supplementary material, which is available to authorized users. BioMed Central 2016-03-31 /pmc/articles/PMC4815194/ /pubmed/27036623 http://dx.doi.org/10.1186/s13059-016-0918-z Text en © Peltzer et al. 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Peltzer, Alexander
Jäger, Günter
Herbig, Alexander
Seitz, Alexander
Kniep, Christian
Krause, Johannes
Nieselt, Kay
EAGER: efficient ancient genome reconstruction
title EAGER: efficient ancient genome reconstruction
title_full EAGER: efficient ancient genome reconstruction
title_fullStr EAGER: efficient ancient genome reconstruction
title_full_unstemmed EAGER: efficient ancient genome reconstruction
title_short EAGER: efficient ancient genome reconstruction
title_sort eager: efficient ancient genome reconstruction
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815194/
https://www.ncbi.nlm.nih.gov/pubmed/27036623
http://dx.doi.org/10.1186/s13059-016-0918-z
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