This directory contains the data of a low-coverage genome from the Neandertal femur found in Hohlenstein-Stadel Cave, Germany. ----------------------- All_sequences ----------------------- Raw sequencing data (unaligned BAM files) from each single-stranded DNA libraries. Base calling was performed using Bustard. Adapter sequences were removed and overlapping forward and reverse reads were merged using leeHom. ----------------------- hg19 ----------------------- Aligned sequences to the human reference genome (hg19). Sequences were aligned with BWA using parameters for ancient DNA "-n 0.01 -o 2 -l 16500". After mapping, sequences starting and ending at identical coordinates (representing PCR duplicates) were collapsed into a single sequence using bam-rmdup (https://bitbucket.org/ustenzel/biohazard). The data was then restricted to mappable regions (Heng Li's 35mer filter: a position is mappable if none of the overlapping 35mers align to any other position in the genome allowing for up to one mismatch) and to sequences with length >= 30 and a mapping quality >= 25. ----------------------- NeandertalizedReference ----------------------- Sequences aligned to both the human reference genome (hg19) and a "Neandertalized" version of hg19. The modified version of hg19 includes alleles that differ between the original hg19 reference and the high-coverage genomes of the Altai Neandertal and Vindija 33.19 (at 3-allelic sites, only one alternative allele was chosen randomly). Raw sequences were aligned to this additional reference (with the same parameters described above) and these alignments were then merged with the original set of alignments to hg19 using bam-mergeRef(https://github.com/StephanePeyregne/bam-mergeRef). As described above, PCR duplicates were then collapsed into a single sequence, sequences outside mappable regions were removed (Heng Li's 35mer filter) and only sequences with length >= 30 and a mapping quality >= 25 were kept. Contact: Email: stephane_peyregne@eva.mpg.de