Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

Mikkel Schubert, Luca Ermini, Clio Der Sarkissian, Hákon Jónsson, Aurélien Ginolhac, Robert Schaefer, Michael D. Martin, Ruth Fernández, Martin Kircher, Molly McCue, Eske Willerslev, Ludovic Orlando*

*Corresponding author for this work

Research output: Contribution to journalArticleResearchpeer-review

288 Citations (Scopus)

Abstract

Next-generation sequencing technologies have revolutionized the field of paleogenomics, allowing the reconstruction of complete ancient genomes and their comparison with modern references. However, this requires the processing of vast amounts of data and involves a large number of steps that use a variety of computational tools. Here we present PALEOMIX (http://geogenetics.ku.dk/ publications/paleomix), a flexible and user-friendly pipeline applicable to both modern and ancient genomes, which largely automates the in silico analyses behind whole-genome resequencing. Starting with next-generation sequencing reads, PALEOMIX carries out adapter removal, mapping against reference genomes, PCR duplicate removal, characterization of and compensation for postmortem damage, SNP calling and maximum-likelihood phylogenomic inference, and it profiles the metagenomic contents of the samples. As such, PALEOMIX allows for a series of potential applications in paleogenomics, comparative genomics and metagenomics. Applying the PALEOMIX pipeline to the three ancient and seven modern Phytophthora infestans genomes as described here takes 5 d using a 16-core server.

Original languageEnglish
Pages (from-to)1056-1082
Number of pages27
JournalNature Protocols
Volume9
Issue number5
DOIs
Publication statusPublished - May 2014
Externally publishedYes

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