Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2014-05

AUTHORS

Mikkel Schubert, Luca Ermini, Clio Der Sarkissian, Hákon Jónsson, Aurélien Ginolhac, Robert Schaefer, Michael D Martin, Ruth Fernández, Martin Kircher, Molly McCue, Eske Willerslev, Ludovic Orlando

ABSTRACT

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. More... »

PAGES

1056-1082

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nprot.2014.063

    DOI

    http://dx.doi.org/10.1038/nprot.2014.063

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1020179577

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/24722405


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