期刊
NATURE PROTOCOLS
卷 9, 期 5, 页码 1056-1082出版社
NATURE PORTFOLIO
DOI: 10.1038/nprot.2014.063
关键词
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资金
- Danish Council for Independent Research, Natural Sciences (FNU)
- Danish National Research Foundation [DNRF94]
- Marie Curie Career Integration [FP7 CIG-293845]
- Marie Curie FP7 Initial Training Network (EUROTAST)
- Lundbeck foundation [R52-A5062]
- Marie Curie Intra-European Fellowships [FP7 IEF-299176, IEF-302617]
- AXA Research Fund [32983]
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.
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