Systematic benchmark of ancient DNA read mapping

Assessing DNA Sequence Alignment Methods for Characterizing Ancient Genomes and Methylomes

(2020) Marine Poullet et al.   Frontiers in Ecology and Evolution

admixr—R package for reproducible analyses using ADMIXTOOLS

(2019) Martin Petr et al.   BIOINFORMATICS

Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology

(2019) Jocelyn Plassais et al.   Nature Communications

The presence and impact of reference bias on population genomic studies of prehistoric human populations

(2019) Torsten Günther et al.   PLoS Genetics

Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe

(2019) Stéphane Peyrégne et al.   Science Advances

Towards pan-genome read alignment to improve variation calling

(2018) Daniel Valenzuela et al.   BMC GENOMICS

Genomic Evidence of Widespread Admixture from Polar Bears into Brown Bears during the Last Ice Age

(2018) James A Cahill et al.   MOLECULAR BIOLOGY AND EVOLUTION

Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool

(2018) Ulrike Taron et al.   Genes

The genome of the offspring of a Neanderthal mother and a Denisovan father

(2018) Viviane Slon et al.   NATURE

Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation

(2018) Éadaoin Harney et al.   Nature Communications

Genome graphs and the evolution of genome inference

(2017) Benedict Paten et al.   GENOME RESEARCH

DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification

(2017) Lixin Chen et al.   SCIENCE

Impact of post-alignment processing in variant discovery from whole exome data

(2016) Shulan Tian et al.   BMC BIOINFORMATICS

Reconstructing ancient genomes and epigenomes

(2015) Ludovic Orlando et al.   NATURE REVIEWS GENETICS

Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data

(2015) Débora Y. C. Brandt et al.   G3-Genes Genomes Genetics

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Ancient human genomes suggest three ancestral populations for present-day Europeans

(2014) Iosif Lazaridis et al.   NATURE

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European

(2014) Iñigo Olalde et al.   NATURE

Partial uracil-DNA-glycosylase treatment for screening of ancient DNA

(2014) N. Rohland et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic structure in Europeans dating back at least 36,200 years

(2014) A. Seguin-Orlando et al.   SCIENCE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Improving the performance of True Single Molecule Sequencing for ancient DNA

(2012) Aurelien Ginolhac et al.   BMC GENOMICS

Improving ancient DNA read mapping against modern reference genomes

(2012) Mikkel Schubert et al.   BMC GENOMICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Evaluation of next-generation sequencing software in mapping and assembly

(2011) Suying Bao et al.   JOURNAL OF HUMAN GENETICS

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Small insertions and deletions (INDELs) in human genomes

(2010) J. M. Mullaney et al.   HUMAN MOLECULAR GENETICS

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

(2009) Adrian W. Briggs et al.   NUCLEIC ACIDS RESEARCH

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS