EAGER: efficient ancient genome reconstruction

Alexander Peltzer,Christian Kniep,Günter Jäger,Kay Nieselt,Johannes Krause,Alexander Seitz,Alexander Herbig

doi:10.1186/s13059-016-0918-z

Abstract

BackgroundThe automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process.ResultsHere 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.ConclusionsEAGER 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 materialThe online version of this article (doi:10.1186/s13059-016-0918-z) contains supplementary material, which is available to authorized users.

Highlights

The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process
We have developed EAGER, a fast and highly user-friendly next-generation sequencing (NGS) analysis pipeline for the efficient reconstruction of ancient genomes, which is designed to be used by researchers without the requirement to apply scripting languages or obtain further programming knowledge
To evaluate the performance of the pipeline and the fundamental tools, EAGER has been applied to six published data sets: five ancient Mycobacterium leprae data sets from Schuenemann et al [2] and a high coverage ancient human genome data set published in Lazaridis et al [19]

Summary

Results

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. EAGER comprises tools to genotype samples to discover, filter, and analyze variants

Conclusions

Background

Results and discussion

Method

Methods