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

Mikkel Schubert; Luca Ermini; Clio Der Sarkissian; Hákon Jónsson; Aurélien Ginolhac; Robert Schaefer; Michael David Martin; Rut Fernandez Garcia; Martin Kircher; Molly McCue; Eske Willerslev; Ludovic Antoine Alexandre Orlando

doi:10.1038/nprot.2014.063

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

Mikkel Schubert, Luca Ermini, Clio Der Sarkissian, Hákon Jónsson, Aurélien Ginolhac, Robert Schaefer, Michael David Martin, Rut Fernandez Garcia, Martin Kircher, Molly McCue, Eske Willerslev, Ludovic Antoine Alexandre Orlando

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

335 Citationer (Scopus)

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.

Originalsprog	Engelsk
Tidsskrift	Nature Protocols
Vol/bind	9
Udgave nummer	5
Sider (fra-til)	1056-82
Antal sider	27
ISSN	1754-2189
DOI	https://doi.org/10.1038/nprot.2014.063
Status	Udgivet - 2014

Adgang til dokumentet

10.1038/nprot.2014.063

Citationsformater

Schubert, M., Ermini, L., Der Sarkissian, C., Jónsson, H., Ginolhac, A., Schaefer, R., Martin, M. D., Fernandez Garcia, R., Kircher, M., McCue, M., Willerslev, E., & Orlando, L. A. A. (2014). Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nature Protocols, 9(5), 1056-82. https://doi.org/10.1038/nprot.2014.063

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. / Schubert, Mikkel; Ermini, Luca; Der Sarkissian, Clio; Jónsson, Hákon; Ginolhac, Aurélien; Schaefer, Robert; Martin, Michael David; Fernandez Garcia, Rut; Kircher, Martin; McCue, Molly; Willerslev, Eske; Orlando, Ludovic Antoine Alexandre.

I: Nature Protocols, Bind 9, Nr. 5, 2014, s. 1056-82.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

Schubert, M, Ermini, L, Der Sarkissian, C, Jónsson, H, Ginolhac, A, Schaefer, R, Martin, MD, Fernandez Garcia, R, Kircher, M, McCue, M, Willerslev, E & Orlando, LAA 2014, 'Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX', Nature Protocols, bind 9, nr. 5, s. 1056-82. https://doi.org/10.1038/nprot.2014.063

Schubert, Mikkel ; Ermini, Luca ; Der Sarkissian, Clio ; Jónsson, Hákon ; Ginolhac, Aurélien ; Schaefer, Robert ; Martin, Michael David ; Fernandez Garcia, Rut ; Kircher, Martin ; McCue, Molly ; Willerslev, Eske ; Orlando, Ludovic Antoine Alexandre. / Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. I: Nature Protocols. 2014 ; Bind 9, Nr. 5. s. 1056-82.

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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.",

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AU - Schubert, Mikkel

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AU - Jónsson, Hákon

AU - Ginolhac, Aurélien

AU - Schaefer, Robert

AU - Martin, Michael David

AU - Fernandez Garcia, Rut

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AU - McCue, Molly

AU - Willerslev, Eske

AU - Orlando, Ludovic Antoine Alexandre

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N2 - 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.

AB - 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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