Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.
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.
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Mikkel
0000000324019921
M
Schubert
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Luca
L
Ermini
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Clio
C
Der Sarkissian
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Hákon
H
Jónsson
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Aurélien
A
Ginolhac
Biomedical Informatics and Computational Biology Graduate Program, University of Minnesota Rochester, Rochester, Minnesota, USA.
Robert
R
Schaefer
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Michael D
MD
Martin
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Ruth
R
Fernández
Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
Martin
0000000192785471
M
Kircher
College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA.
Molly
M
McCue
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Eske
E
Willerslev
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Ludovic
L
Orlando
D019295:Computational Biology / Q000379:methods*; D016678:Genome / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D016013:Likelihood Functions; D056186:Metagenomics / Q000379:methods*; D010163:Paleontology / Q000379:methods*; D010802:Phylogeny; D055750:Phytophthora infestans / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012984:Software