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

By Mikkel Schubert, L. Ermini, C. D. Sarkissian, Hákon Jónsson, Aurelien Ginolhac, R. Schaefer, Michael D. Martin, Ruth Fernández, Martin Kircher, M. McCue and 2 more. Nature Protocols, 2014

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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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/d0873f0d1f7624e510ce01b0e7c54adc0930e060

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In Molecular Biology

Citations in the corpus

EAGER: efficient ancient genome reconstruction (2016, methodology): “Previously published protocols, such as PALEOMIX [10], partially overlap in terms of features; however, EAGER offers an improved user experience by providing a GUI, swift setup, and short processing time.”
Ancient DNA (2019, methodology): “When using high-throughput sequencing approaches, exploring the diversity of sequences preserved within the sample or extract, such as using MEGAN [44], can provide additional information about the preservation, contamination, and authenticity.”
Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections (2018, methodology): “In addition to improvements in recovering genetic data from historical herbarium specimens, new computational pipelines such as PALEOMIX (Schubert et al. 2014), EAGER (Peltzer et al. 2016), and ATLAS (Link et al. 2017) have been developed specifically for genomic data from degraded specimens.”
Single‐tube library preparation for degraded DNA (2017, methodology): “Data Processing The initial bioinformatics processing of the sequencing reads was based on the Paleomix pipeline (Schubert et al. 2014).”