Paleomix – University of Copenhagen

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The Paleomix Group and Next Generation Sequencing

Up until a few years ago, sequencing complete genomes still represented a massive endeavor involving hundreds of researchers and thousands of sequencing machines grouped within big sequencing centres.

The advent of next generation sequencing machines has completely changed this situation, by delivering up to billions of sequences within a couple of weeks. As a result, we now know the genomic sequence of a variety of taxa, including non-model organisms, and even those of extinct species and ancient individuals.

For some groups such as humans, we even know the sequence variation segregating at the genome scale in a large number of populations around the world. The fantastic throughput of next-generation sequencing platforms has reduced sequencing costs by orders of magnitude, but has at the same time increased the computational workload associated with the characterization of full genome sequences.

The PALEOMIX pipeline

The PALEOMIX pipeline is a user-friendly package designed for Unix-like systems and largely automates the analyses related to whole genome re-sequencing. It is compatible with a full range of sequence data and performs a series of user-defined analyses, including read trimming, collapsing of overlapping mate-pairs, read mapping, PCR duplicate removal, SNP calling, and metagenomic profiling.

For ancient DNA sequence data, the PALEOMIX pipeline also supports the quantification of post-mortem DNA damage and standard mis-incorporation and fragmentation patterns. Finally, in situations where several genomes are available, the PALEOMIX pipeline can reconstruct Maximum Likelihood phylogenomic trees and reveal the evolutionary phylogenetic relationships among taxa.

The PALEOMIX pipeline has been developed by researchers from Ludovic Orlando’s group at the Centre for GeoGenetics, University of Copenhagen, Denmark. The software and related documentation is available at

A paper documenting the PALEOMIX pipeline was published in Nature Protocols, see 
Schubert M, Ermini L, Sarkissian CD, Jónsson H, Ginolhac A, Schaefer R, Martin MD, Fernández R, Kircher M, McCue M, Willerslev E, and Orlando L. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat Protoc. 2014 May;9(5):1056-82. doi: 10.1038/nprot.2014.063. Epub 2014 Apr 10. PubMed PMID: 24722405.

See the news item from 25. April 2014.

This work was supported by the Danish Council for Independent Research, Natural Sciences (FNU); the Danish National Research Foundation (DNRF94); a Marie-Curie Career Integration grant (FP7 CIG-293845); the Lundbeck foundation (R52-A5062).