Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX
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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.
In: Nature Protocols, Vol. 9, No. 5, 2014, p. 1056-82.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX
AU - Schubert, Mikkel
AU - Ermini, Luca
AU - Der Sarkissian, Clio
AU - Jónsson, Hákon
AU - Ginolhac, Aurélien
AU - Schaefer, Robert
AU - Martin, Michael David
AU - Fernandez Garcia, Rut
AU - Kircher, Martin
AU - McCue, Molly
AU - Willerslev, Eske
AU - Orlando, Ludovic Antoine Alexandre
PY - 2014
Y1 - 2014
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 (https://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 (https://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.
U2 - 10.1038/nprot.2014.063
DO - 10.1038/nprot.2014.063
M3 - Journal article
C2 - 24722405
VL - 9
SP - 1056
EP - 1082
JO - Nature Protocols
JF - Nature Protocols
SN - 1754-2189
IS - 5
ER -
ID: 128558987