Simulated read data analysed in "Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph"

<p>Simulated read data analyzed in &quot;Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph&quot;.</p> <p><strong>1) Human sequence data</strong></p> <p><strong>HO_chr11_50bp_sliding_window*fq.gz:</strong><br> All possible 50 bp reads overlapping chromosome 11 SNPs in the Human Origins dataset. Files with the word &quot;alternate&quot; in their filename carry the alternate allele, otherwise, they carry the reference allele. Deamination has been added into these simulated reads using gargammel (Renaud 2016) based on empirically estimated post-mortem damage in a dataset of 102 ancient genomes (Allentoft et al., 2015).</p> <p><strong>2) microbial data</strong></p> <p><strong>simulation_*_s.fq.gz:</strong><br> Simulated microbial read data&nbsp;from a set of microbial reference genomes identified in the ancient Clovis genome (Rasmussen 2014), using gargammel.</p>