Data

Yersinia pestis genomes from 4,000 year-old sites in Britain

https://www.ebi.ac.uk/ena/browser/view/PRJEB61230

Ancient genomes of two 13,000-15,000 year old humans from Britain (Charlton, Brace, Hajdinjak et al. 2022, Nature Ecology and Evolution):
https://www.ebi.ac.uk/ena/browser/view/PRJEB52727

Ancient genomes of 65 ancient wolves (Bergström, Stanton, Taron et al. 2022, Nature)
BAM and FASTQ files: https://www.ebi.ac.uk/ena/browser/view/PRJEB42199

Ancient genomes of 27 early dogs (Bergstrom et al. 2020, Science):
BAM and FASTQ files: https://www.ebi.ac.uk/ena/browser/view/PRJEB38079

Ancient genome of a 34,900 year-old Siberian wolf (Skoglund et al. 2015, Current Biology)
BAM file of reads mapping to canFam3: [0.7x, USER-treated] [0.3x, non-USER treated]

FASTA-file of mtDNA consensus: [182x, USER-treated]

FASTQ-files: [ENA link]

Tools

POPSTATS: a program to compute symmetry tests and other summary statistics on whole-genome data from humans and other organisms: https://github.com/pontussk/popstats (Skoglund et al. 2015, Nature)
PMDtools: a likelihood-based approach for separating ancient DNA from modern-day contamination. See the PMDtools page: https://github.com/pontussk/PMDtools (Skoglund et al. 2014, PNAS)
Ry_compute: a method for inferring biological sex from ancient genomic sequences. Available here: https://github.com/pontussk/ry_compute (original [download]) (Skoglund et al. 2014, JAS)