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glactools: a command-line toolset for the management of genotype likelihoods and allele counts.. Bioinform., 34 (8): 1398-1400 (2018)freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers., , , and . Bioinform., 29 (9): 1208-1209 (2013)trieFinder: an efficient program for annotating digital gene expression (DGE) tags., , , , and . BMC Bioinform., (2014)A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data., , , , , , and . Bioinform., 36 (3): 828-841 (2020)HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph., , , , and . PLoS Comput. Biol., (2023)Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans, , and . PLOS Genetics, 12 (4): 1-27 (April 2016)deML: robust demultiplexing of Illumina sequences using a likelihood-based approach., , , , and . Bioinform., 31 (5): 770-772 (2015)gargammel: a sequence simulator for ancient DNA., , , and . Bioinform., 33 (4): 577-579 (2017)Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees., , , , , , and . BMC Bioinform., (2009)Ancient human genomes suggest three ancestral populations for present-day Europeans, , , , , , , , , and 88 other author(s). (2013)