Abstract
Over the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of captured SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain types of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw reads. This task is computationally intensive. Here, we release a dataset including 35 whole-genome sequenced samples, previously published and distributed worldwide, together with the genetic pipeline used to process them. The dataset contains 72,041,355 sites called across 19 ancient and 16 modern individuals and includes sequence data from four previously published ancient samples which we sequenced to higher coverage (10–18x). Such a resource will allow researchers to analyse their new samples with the same genetic pipeline and directly compare them to the reference dataset without re-processing published samples. Moreover, this dataset can be easily expanded to increase the sample distribution both across time and space.
Highlights
Background & SummaryThe number of ancient humans with genome-wide data available has increased from less than five a decade ago to more than 3,000 thanks to advancements in extraction and sequencing methods for ancient DNA[1]
The final dataset includes 35 samples with 509,351,727 sites in neutral regions before filtering
Sites not called across all samples
Summary
The number of ancient humans with genome-wide data available has increased from less than five a decade ago to more than 3,000 thanks to advancements in extraction and sequencing methods for ancient DNA (aDNA)[1]. Researchers have to download raw reads of published samples and reprocess them to create a dataset to compare their new samples against without pipeline-associated biases. This problem is less pronounced for modern DNA samples as the higher quality of DNA and sequencing coverage partially reduce the biases introduced by the usage of different bioinformatic tools. We fully reprocessed high-quality shotgun sequenced ancient samples downloaded from the literature, generated additional new data for previously published 4 ancient samples and merged them with modern samples. The final dataset includes 35 individuals and researchers can use it to quickly compare their new samples against a set of individuals distributed across time and space (Fig. 1). Sample_ID SS6004477 LP6005443-DNA_B09 LP6005443-DNA_B03 LP6005519-DNA_D05 LP6005443-DNA_D04 LP6005441-DNA_G06 LP6005441-DNA_E07 LP6005443-DNA_G04 LP6005441-DNA_F09 LP6005443-DNA_D08 LP6005441-DNA_F10 LP6005442-DNA_H12 LP6005442-DNA_D01 LP6005442-DNA_F01 LP6005442-DNA_B02 JHM06
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