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.
Bibliographical noteFunding Information:
acknoWleDGMents 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); and the Marie Curie FP7 Initial Training Network (EUROTAST). The work of M.S. was made possible thanks to the support of the Lundbeck foundation (R52-A5062). A.G. and L.E. were supported by Marie Curie Intra-European Fellowships (FP7 IEF-299176 and IEF-302617, respectively). R.F. was supported by a postdoctoral grant from AXA Research Fund (32983).