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dc.contributor.authorSchubert, Mikkel
dc.contributor.authorErmini, Luca
dc.contributor.authorDer Sarkissian, Clio
dc.contributor.authorJonsson, Hakon
dc.contributor.authorGinolhac, Aurelien
dc.contributor.authorSchaefer, Robert
dc.contributor.authorMartin, Michael D.
dc.contributor.authorFernandez, Ruth
dc.contributor.authorKircher, Martin
dc.contributor.authorMcCue, Molly
dc.contributor.authorWillerslev, Eske
dc.contributor.authorOrlando, Ludovic
dc.date.accessioned2017-12-08T03:45:40Z
dc.date.available2017-12-08T03:45:40Z
dc.date.issued2014
dc.identifier.issn1754-2189
dc.identifier.doi10.1038/nprot.2014.063
dc.identifier.urihttp://hdl.handle.net/10072/172204
dc.description.abstractNext-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.
dc.description.peerreviewedYes
dc.languageEnglish
dc.language.isoeng
dc.publisherNature Publishing Group
dc.relation.ispartofpagefrom1056
dc.relation.ispartofpageto1082
dc.relation.ispartofissue5
dc.relation.ispartofjournalNature Protocols
dc.relation.ispartofvolume9
dc.subject.fieldofresearchGenetics not elsewhere classified
dc.subject.fieldofresearchChemical Sciences
dc.subject.fieldofresearchBiological Sciences
dc.subject.fieldofresearchMedical and Health Sciences
dc.subject.fieldofresearchcode060499
dc.subject.fieldofresearchcode03
dc.subject.fieldofresearchcode06
dc.subject.fieldofresearchcode11
dc.titleCharacterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
gro.hasfulltextNo Full Text
gro.griffith.authorWillerslev, Eske


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