Analysis of High-Throughput Ancient DNA Sequencing Data
Abstract
Advances in sequencing technologies have dramatically changed the field of ancient DNA (aDNA). It is now possible to generate an enormous quantity of aDNA sequence data both rapidly and inexpensively. As aDNA sequences are generally short in length, damaged, and at low copy number relative to coextracted environmental DNA, high-throughput approaches offer a tremendous advantage over traditional sequencing approaches in that they enable a complete characterization of an aDNA extract. However, the particular qualities of aDNA also present specific limitations that require careful consideration in data analysis. For example, results of high-throughout analyses of aDNA libraries may include chimeric sequences, sequencing error and artifacts, damage, and alignment ambiguities due to the short read lengths. Here, I describe typical primary data analysis workflows for high-throughput aDNA sequencing experiments, including (1) separation of individual samples in multiplex experiments; (2) removal of protocol-specific library artifacts; (3) trimming adapter sequences and merging paired-end sequencing data; (4) base quality score filtering or quality score propagation during data analysis; (5) identification of endogenous molecules from an environmental background; (6) quantification of contamination from other DNA sources; and (7) removal of clonal amplification products or the compilation of a consensus from clonal amplification products, and their exploitation for estimation of library complexity.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Decreasing the -n edit distance parameter in bwa aln from the default value of 0.04 to 0.02 or 0.01 allows more mismatches and increases sensitivity.
“decreasing the -n edit distance parameter from the default value of 0.04 to 0.02 [13] or 0.01 [14] allows more mismatches and increases sensitivity”
From Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph (2020) · cites this paper as [14]
Using bwa aln with very relaxed parameters (-n 0.01 -o 2) in combination with disabling seeding (-l 1024) and mapQ 25 filtering had a beneficial impact in sensitivity (99.60% vs 97.34% for mapping reads containing the alternate allele) and a more balanced alternate allele representation (0.49936) but also increases error rates, for example increasing the rate of false mapping short microbial reads
“This had a beneficial impact in terms of sensitivity (99.60% vs 97.34% for the mapping of reads containing the alternate allele) and a more balanced alternate allele representation (0.49936) but also increases error rates, for example increasing the rate of false mapping short microbial reads (Additional file 1: Fig. S9).”
From Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph (2020) · cites this paper as [14]
Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617 · see citing works
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662 · see citing works
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · see citing works
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849 · see citing works
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,617 · see citing works
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Li, W.-Z., & Godzik, A. (2006) · Bioinform. · doi:10.1093/bioinformatics/btl158 · Cited by 10,994 · see citing works
Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,387 · see citing works
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480 · see citing works
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693 · see citing works
T-Coffee: A novel method for fast and accurate multiple sequence alignment.
Notredame, C., Higgins, D., & Heringa, J. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4042 · Cited by 7,321 · see citing works
Biopython: freely available python tools for computational molecular biology and bioinformatics
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp163 · Cited by 6,080 · see citing works
A Greedy Algorithm for Aligning DNA Sequences
Zhang, Z., Schwartz, S., Wagner, L., & Miller, W. (2000) · Journal of Computational Biology · doi:10.1089/10665270050081478 · Cited by 5,459 · see citing works
Base-Calling of Automated Sequencer Traces Using <i>Phred.</i> II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439 · see citing works
Next-generation DNA sequencing
Shendure, J., & Ji, H. (2008) · Nature Biotechnology · doi:10.1038/nbt1486 · Cited by 4,509 · see citing works
A draft sequence of the Neandertal genome
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318 · see citing works
Self-citationSOAP2: an improved ultrafast tool for short read alignment
Li, R., Yu, C., Li, Y., Lam, T., Yiu, S., Kristiansen, K., & Wang, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp336 · Cited by 3,763 · see citing works
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684 · see citing works
SOAP: Short oligonucleotide alignment program
Li, R., Li, Y., Kristiansen, K., & Wang, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn025 · Cited by 3,597 · see citing works
Chang, F. W., Dean, J., Ghemawat, S., Hsieh, W. C.-Y., Wallach, D. A., Burrows, M., Chandra, T., Fikes, A., & Gruber, R. E. (2008) · ACM Transactions on Computer Systems · doi:10.1145/1365815.1365816 · Cited by 3,461 · see citing works
Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and SequencingPreprint
Meyer, M., & Kircher, M. (2010) · Cold Spring Harbor Protocols · doi:10.1101/pdb.prot5448 · Cited by 2,233 · see citing works
Self-citationGenetic history of an archaic hominin group from Denisova Cave in Siberia
Reich, D., Green, R. E., Kircher, M., Krause, J., Patterson, N., Durand, E. Y., Viola, B., Briggs, A. W., Stenzel, U., Johnson, P. L. F., et al. (2010) · Nature · doi:10.1038/nature09710 · Cited by 1,991 · see citing works
Self-citationThe Bioperl Toolkit: Perl Modules for the Life SciencesPreprint
Stajich, J., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G. R., Korf, I. F., Lapp, H., et al. (2002) · Genome Research · doi:10.1101/gr.361602 · Cited by 1,642 · see citing works
Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome
Shendure, J., Porreca, G. J., Reppas, N. B., Lin, X., McCutcheon, J. P., Rosenbaum, A. M., Wang, M. D., Zhang, K., Mitra, R. D., & Church, G. M. (2005) · Science · doi:10.1126/science.1117389 · Cited by 1,402 · see citing works
Database indexing for production MegaBLAST searches
Morgulis, A. O., Coulouris, G., Raytselis, Y., Madden, T., Agarwala, R., & Schäffer, A. A. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn322 · Cited by 1,352 · see citing works
Target-enrichment strategies for next-generation sequencing
Mamanova, L., Coffey, A. J., Scott, C. E., Kozarewa, I., Turner, E. H., Kumar, A., Howard, E. K., Shendure, J., & Turner, D. (2010) · Nature Methods · doi:10.1038/nmeth.1419 · Cited by 1,221 · see citing works
Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays
Drmanac, R., Sparks, A. B., Callow, M. J., Halpern, A. L., Burns, N. L., Kermani, B. G., Carnevali, P., Nazarenko, I., Nilsen, G. B., Yeung, G., et al. (2010) · Science · doi:10.1126/science.1181498 · Cited by 1,212 · see citing works
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
Dohm, J. C., Lottaz, C., Borodina, T., & Himmelbauer, H. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn425 · Cited by 1,088 · see citing works
Patterns of damage in genomic DNA sequences from a neandertal
Briggs, A. W., Stenzel, U., Johnson, P. L. F., Green, R. E., Kelso, J., Prüfer, K., Meyer, M., Krause, J., Ronan, M. T., Lachmann, M., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704665104 · Cited by 981 · see citing works
Ancient human genome sequence of an extinct Palaeo-Eskimo
Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., et al. (2010) · Nature · doi:10.1038/nature08835 · Cited by 849 · see citing works
The complete mitochondrial DNA genome of an unknown hominin from southern Siberia
Krause, J., Fu, Q., Good, J. M., Viola, B., Shunkov, M. V., Derevianko, A. P., & Pääbo, S. (2010) · Nature · doi:10.1038/nature08976 · Cited by 792 · see citing works
Single-Molecule DNA Sequencing of a Viral Genome
Harris, T. D., Buzby, P. R., Babcock, H. P., Beer, E., Bowers, J., Braslavsky, I., Causey, M., Colonell, J. I., Dimeo, J. J., Efcavitch, J. W., et al. (2008) · Science · doi:10.1126/science.1150427 · Cited by 692 · see citing works
Hofreiter, M. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.23.4793 · Cited by 684 · see citing works
High‐throughput DNA sequencing – concepts and limitations
Kircher, M., & Kelso, J. F. (2010) · BioEssays · doi:10.1002/bies.200900181 · Cited by 675 · see citing works
Self-citationMetagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA
Poinar, H. N., Schwarz, C., Qi, J., Shapiro, B., MacPhee, R. D. E., Buigues, B., Tikhonov, A., Huson, D. H., Tomsho, L. P., Auch, A. F., et al. (2005) · Science · doi:10.1126/science.1123360 · Cited by 618 · see citing works
A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing
Green, R. E., Malaspinas, A., Krause, J., Briggs, A. W., Johnson, P. L. F., Uhler, C., Meyer, M., Good, J. M., Maričić, T., Stenzel, U., et al. (2008) · Cell · doi:10.1016/j.cell.2008.06.021 · Cited by 601 · see citing works
Meyerhans, A., Vartanian, J., & Wain–Hobson, S. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.7.1687 · Cited by 578 · see citing works
Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes
Briggs, A. W., Good, J. M., Green, R. E., Krause, J., Maričić, T., Stenzel, U., Lalueza‐Fox, C., Rudan, P., Brajković, D., Kućan, Ž., et al. (2009) · Science · doi:10.1126/science.1174462 · Cited by 501 · see citing works
DNA damage promotes jumping between templates during enzymatic amplification.
Pääbo, S., Irwin, D. M., & Wilson, A. C. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)39621-8 · Cited by 499 · see citing works
Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA
Briggs, A. W., Stenzel, U., Meyer, M., Krause, J., Kircher, M., & Pääbo, S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1163 · Cited by 491 · see citing works
Self-citationDe novo transcriptome assembly with ABySS
Birol, İ., Jackman, S. D., Nielsen, C. B., Qian, J. Q., Varhol, R., Stazyk, G., Morin, R. D., Zhao, Y., Hirst, M., Schein, J. E., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp367 · Cited by 400 · see citing works
Using quality scores and longer reads improves accuracy of Solexa read mapping
Smith, A. D., Xuan, Z., & Zhang, M. Q. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-128 · Cited by 374 · see citing works
Sequencing the nuclear genome of the extinct woolly mammoth
Miller, W., Drautz, D. I., Ratan, A., Pusey, B. N., Qi, J., Lesk, A. M., Tomsho, L. P., Packard, M., Zhao, F., Sher, A. V., et al. (2008) · Nature · doi:10.1038/nature07446 · Cited by 345 · see citing works
Parallel tagged sequencing on the 454 platform
Meyer, M., Stenzel, U., & Hofreiter, M. (2008) · Nature Protocols · doi:10.1038/nprot.2007.520 · Cited by 324 · see citing works
How to map billions of short reads onto genomes
Trapnell, C., & Salzberg, S. L. (2009) · Nature Biotechnology · doi:10.1038/nbt0509-455 · Cited by 307 · see citing works
A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia
Krause, J., Briggs, A. W., Kircher, M., Maričić, T., Zwyns, N., Derevianko, A. P., & Pääbo, S. (2010) · Current Biology · doi:10.1016/j.cub.2009.11.068 · Cited by 290 · see citing works
Self-citationExpression profiling of microRNAs by deep sequencing
Creighton, C. J., Reid, J. G., & Gunaratne, P. H. (2009) · Briefings in Bioinformatics · doi:10.1093/bib/bbp019 · Cited by 289 · see citing works
De novo fragment assembly with short mate-paired reads: Does the read length matter?
Chaisson, M. J., Brinza, D., & Pevzner, P. A. (2009) · Genome Research · doi:10.1101/gr.079053.108 · Cited by 279 · see citing works
Artificial and natural duplicates in pyrosequencing reads of metagenomic data
Niu, B., Fu, L., Sun, S., & Li, W. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-187 · Cited by 278 · see citing works
Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture
Burbano, H. A., Hodges, E. C., Green, R. E., Briggs, A. W., Krause, J., Meyer, M., Good, J. M., Maričić, T., Johnson, P. L. F., Xuan, Z., et al. (2010) · Science · doi:10.1126/science.1188046 · Cited by 276 · see citing works
Improved base calling for the Illumina Genome Analyzer using machine learning strategies
Kircher, M., Stenzel, U., & Kelso, J. F. (2009) · Genome biology · doi:10.1186/gb-2009-10-8-r83 · Cited by 271 · see citing works
Self-citationExtending assembly of short DNA sequences to handle error
Jeck, W. R., Reinhardt, J. A., Baltrus, D. A., Hickenbotham, M. T., Magrini, V. J., Mardis, E. R., Dangl, J. L., & Jones, C. D. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm451 · Cited by 269 · see citing works
Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae
Krause, J., Dear, P. H., Pollack, J. L., Slatkin, M., Spriggs, H. F., Barnes, I., Lister, A. M., Ebersberger, I., Pääbo, S., & Hofreiter, M. (2005) · Nature · doi:10.1038/nature04432 · Cited by 244 · see citing works
Korlach, J., Marks, P., Cicero, R. L., Gray, J. J., Murphy, D. L., Roitman, D. B., Pham, T. T., Otto, G. A., Foquet, M., & Turner, S. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0710982105 · Cited by 236 · see citing works
TagDust—a program to eliminate artifacts from next generation sequencing data
Lassmann, T., Hayashizaki, Y., & Daub, C. O. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp527 · Cited by 228 · see citing works
Alta-Cyclic: a self-optimizing base caller for next-generation sequencing
Erlich, Y., Mitra, P. P., delaBastide, M., McCombie, W. R., & Hannon, G. J. (2008) · Nature Methods · doi:10.1038/nmeth.1230 · Cited by 216 · see citing works
Pyrobayes: an improved base caller for SNP discovery in pyrosequences
Quinlan, A. R., Stewart, D. A., Strömberg, M. P., & Marth, G. (2008) · Nature Methods · doi:10.1038/nmeth.1172 · Cited by 209 · see citing works
The neandertal genome and ancient DNA authenticity
Green, R. E., Briggs, A. W., Krause, J., Prüfer, K., Burbano, H. A., Siebauer, M., Lachmann, M., & Pääbo, S. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.222 · Cited by 190 · see citing works
Lahr, D. J. G., & Katz, L. A. (2009) · BioTechniques · doi:10.2144/000113219 · Cited by 189 · see citing works
Template-switching during DNA synthesis byThermus aquaticusDNA polymerase I
Odelberg, S. J., Weiss, R. B., Hata, A., & White, R. L. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.11.2049 · Cited by 166 · see citing works
Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes
Gilbert, M. T. P., Drautz, D. I., Lesk, A. M., Ho, S. Y. W., Qi, J., Ratan, A., Hsu, C.-H., Sher, A. V., Dalén, L., Götherström, A., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0802315105 · Cited by 162 · see citing works
Computational challenges in the analysis of ancient DNA
Prüfer, K., Stenzel, U., Hofreiter, M., Pääbo, S., Kelso, J., & Green, R. E. (2010) · Genome Biology · doi:10.1186/gb-2010-11-5-r47 · Cited by 155 · see citing works
Stiller, M., Knapp, M., Stenzel, U., Hofreiter, M., & Meyer, M. (2009) · Genome Research · doi:10.1101/gr.095760.109 · Cited by 122 · see citing works
Swift: primary data analysis for the Illumina Solexa sequencing platform
Whiteford, N. E., Skelly, T., Curtis, C. N., Ritchie, M. E., Löhr, A., Zaranek, A. W., Abnizova, I., & Brown, C. G. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp383 · Cited by 105 · see citing works
BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencingPreprint
Kao, W., Stevens, K., & Song, Y. S. (2009) · Genome Research · doi:10.1101/gr.095299.109 · Cited by 91 · see citing works
Heyn, P., Stenzel, U., Briggs, A. W., Kircher, M., Hofreiter, M., & Meyer, M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq572 · Cited by 56 · see citing works
Self-citationTileQC: A system for tile-based quality control of Solexa data
Dolan, P. C., & Denver, D. R. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-250 · Cited by 38 · see citing works
Palmer, L. E., Dejori, M., Bolanos, R. A., et al. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-33 · Cited by 22 · see citing works
Standardizing the Next Generation of Bioinformatics Software Development with BioHDF (HDF5)
Mason, C. E., Zumbo, P., Sanders, S., Folk, M., Robinson, D. E., Aydt, R. A., Gollery, M., Welsh, M., Olson, N. E., & Smith, T. M. F. (2010) · Advances in experimental medicine and biology · doi:10.1007/978-1-4419-5913-3_77 · Cited by 20 · see citing works
Cygwin32: a free win32 porting layer for UNIX® applications
Noer, G. J. (1998) · Conference on USENIX Windows NT Symposium · Cited by 19 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
The complete genome sequence of a Neanderthal from the Altai Mountains
Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature12886 · Cited by 2,254 · see citing works
Self-citationA high-coverage genome sequence from an archaic denisovan individual
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967 · see citing works
Self-citationDabney, J., Knapp, M., Glocke, I., Gansauge, M.-T., Weihmann, A., Nickel, B., Valdiosera, C., García, N., Pääbo, S., Arsuaga, J.-L., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1314445110 · Cited by 1,443 · see citing works
Ancient human genomes suggest three ancestral populations for present-day Europeans
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature · doi:10.1038/nature13673 · Cited by 1,357 · see citing works
DNA analysis of an early modern human from Tianyuan Cave, China
Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H. A., Kelso, J., & Pääbo, S. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1221359110 · Cited by 608 · see citing works
A mitochondrial genome sequence of a hominin from Sima de los Huesos
Meyer, M., Fu, Q., Aximu-Petri, A., Glocke, I., Nickel, B., Arsuaga, J.-L., Martínez, I., Gracia, A., de Castro, J. M. B., Carbonell, E., et al. (2014) · Nature · doi:10.1038/nature12788 · Cited by 534 · see citing works
Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
Schlebusch, C. M., Malmström, H., Günther, T., Sjödin, P., Coutinho, A., Edlund, H., Munters, A. R., Vicente, M., Steyn, M., Soodyall, H., et al. (2017) · Science · doi:10.1126/science.aao6266 · Cited by 519 · see citing works
Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal
Skoglund, P., Northoff, B. H., Shunkov, M. V., Derevianko, A. P., Pääbo, S., Krause, J., & Jakobsson, M. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1318934111 · Cited by 499 · see citing works
Archaeogenomic evidence reveals prehistoric matrilineal dynasty
Kennett, D. J., Plog, S., George, R. J., Culleton, B. J., Watson, A. S., Skoglund, P., Rohland, N., Mallick, S., Stewardson, K., Kistler, L., et al. (2017) · Nature Communications · doi:10.1038/ncomms14115 · Cited by 301 · see citing works
Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques
Günther, T., Valdiosera, C., Malmström, H., Ureña, I., Rodriguez-Varela, R., Sverrisdóttir, Ó. O., Daskalaki, E. A., Skoglund, P., Naidoo, T., Svensson, E. M., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1509851112 · Cited by 278 · see citing works
Günther, T., & Nettelblad, C. (2019) · PLOS Genetics · doi:10.1371/journal.pgen.1008302 · Cited by 228 · see citing works
Cahill, J. A., Green, R. E., Fulton, T. L., Stiller, M., Jay, F., Ovsyanikov, N., Salamzade, R., St. John, J., Stirling, I., Slatkin, M., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003345 · Cited by 221 · see citing works
2000 Years of Parallel Societies in Stone Age Central Europe
Bollongino, R., Nehlich, O., Richards, M. P., Orschiedt, J., Thomas, M. G., Sell, C., Fajkošová, Z., Powell, A., & Burger, J. (2013) · Science · doi:10.1126/science.1245049 · Cited by 195 · see citing works
Martiniano, R., Garrison, E., Jones, E. R., Manica, A., & Durbin, R. (2020) · Genome Biology · doi:10.1186/s13059-020-02160-7 · Cited by 128 · see citing works
Joint estimates of heterozygosity and runs of homozygosity for modern and ancient samples
Renaud, G., Hanghøj, K., Korneliussen, T. S., Willerslev, E., & Orlando, L. (2019) · Genetics · doi:10.1534/genetics.119.302057 · Cited by 101 · see citing works
Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences
de Filippo, C., Meyer, M., & Prüfer, K. (2018) · BMC Biology · doi:10.1186/s12915-018-0581-9 · Cited by 53 · see citing works
Liang, S.-A., Ren, T., Zhang, J., He, J., Wang, X., Jiang, X., He, Y., McCoy, R. C., Fu, Q., Akey, J. M., et al. (2025) · Genome Biology · doi:10.1186/s13059-025-03502-z · Cited by 8 · see citing works
- Authors
- Kircher, M.
- Affiliations
- Max Planck Institute for Evolutionary Anthropology (DE)
- Corresponding author
- Kircher, Martin
- ORCID
- Kircher, Martin
- Venue
- Methods in Molecular Biology
- Publisher
- Humana Press
- Published
- 2011-12-08
- Volume
- 840
- Pages
- 197-228
- ISSN
- 1064-3745 (ISSN-L)
- 1940-6029
- OpenAlex
- W1507075706
- Cited by
- 236
- References
- 73
- Citations by year
- 2026: 9 · 2025: 24 · 2024: 13 · 2023: 16 · 2022: 19 · 2021: 19 · 2020: 26 · 2019: 19 · 2018: 23 · 2017: 13 · 2016: 15 · 2015: 10 · 2014: 15 · 2013: 13 · 2012: 1
- FWCI
- 12.42
- Type
- book chapter
- Language
- en
- Open access
- closed
- Licence
- Locations
- Methods in molecular biology (publishedVersion)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Max-Planck-Institut für Evolutionäre Anthropologie
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Keywords
- ancient DNA, next-generation sequencing, sequencing data analysis, chimeric sequences, sequencing artifacts, adapter trimming, contamination quantification, clonal amplification, consensus sequence, library complexity, multiplexed sequencing, sample separation
- MeSH terms
- Base Sequence, DNA, Fossils, Molecular Sequence Data, Software, Gene Library, Sequence Analysis, DNA, High-Throughput Nucleotide Sequencing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
