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

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

1) Human sequence data

HO_chr11_50bp_sliding_window*fq.gz:
All possible 50 bp reads overlapping chromosome 11 SNPs in the Human Origins dataset. Files with the word "alternate" 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).

2) microbial data

simulation_*_s.fq.gz:
Simulated microbial read data from a set of microbial reference genomes identified in the ancient Clovis genome (Rasmussen 2014), using gargammel.