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Nat Protoc. 2014 May;9(5):1056-82. doi: 10.1038/nprot.2014.063. Epub 2014 Apr 10.

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

Author information

1
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
2
Biomedical Informatics and Computational Biology Graduate Program, University of Minnesota Rochester, Rochester, Minnesota, USA.
3
Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
4
College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA.

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.

PMID:
24722405
DOI:
10.1038/nprot.2014.063
[Indexed for MEDLINE]

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