Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies
暂无分享,去创建一个
Francesco Vezzi | Katerina Guschanski | Tom van der Valk | Love Dalén | F. Vezzi | K. Guschanski | L. Dalén | M. Ormestad | T. van der Valk | Mattias Ormestad | Tom van der Valk
[1] B. Berger,et al. Ancient human genomes suggest three ancestral populations for present-day Europeans , 2013, Nature.
[2] Sharon L. Grim,et al. Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys , 2014, PloS one.
[3] Mattias Jakobsson,et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana , 2014, Nature.
[4] L. Rieseberg,et al. A novel post hoc method for detecting index switching finds no evidence for increased switching on the Illumina HiSeq X. , 2018, Molecular ecology resources.
[5] L. Weyrich,et al. From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era , 2017 .
[6] Mauricio O. Carneiro,et al. From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.
[7] L. Rieseberg,et al. A novel post hoc method for detecting index switching finds no evidence for increased switching on the Illumina HiSeq X , 2017, bioRxiv.
[8] Stinus Lindgreen,et al. AdapterRemoval v2: rapid adapter trimming, identification, and read merging , 2016, BMC Research Notes.
[9] T. Candresse,et al. Phytovirome Analysis of Wild Plant Populations: Comparison of Double-Stranded RNA and Virion-Associated Nucleic Acid Metagenomic Approaches , 2019, Journal of Virology.
[10] Janet Kelso,et al. deML: robust demultiplexing of Illumina sequences using a likelihood-based approach , 2014, Bioinform..
[11] Philip L. F. Johnson,et al. The complete genome sequence of a Neandertal from the Altai Mountains , 2013, Nature.
[12] S. Odelberg,et al. Template-switching during DNA synthesis by Thermus aquaticus DNA polymerase I. , 1995, Nucleic acids research.
[13] Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas , 2018, Scientific Reports.
[14] Colleen R. Stephens,et al. Recent divergences and size decreases of eastern gorilla populations , 2014, Biology Letters.
[15] M. Meyer,et al. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA , 2013, Nature Protocols.
[16] Katerina Guschanski,et al. Whole mitochondrial genome capture from faecal samples and museum‐preserved specimens , 2017, Molecular ecology resources.
[17] Adrian W. Briggs,et al. The Neandertal genome and ancient DNA authenticity , 2009, The EMBO journal.
[18] Matthew J. Huentelman,et al. IDENTIFICATION OF GENETIC VARIANTS USING BARCODED MULTIPLEXED SEQUENCING , 2008, Nature Methods.
[19] Philippe Esling,et al. Accurate multiplexing and filtering for high-throughput amplicon-sequencing , 2015, Nucleic acids research.
[20] Heng Li,et al. Genome sequence of a 45,000-year-old modern human from western Siberia , 2014, Nature.
[21] M. DePristo,et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.
[22] M. Rowicka,et al. Strategies for Achieving High Sequencing Accuracy for Low Diversity Samples and Avoiding Sample Bleeding Using Illumina Platform , 2015, PloS one.
[23] Swapan Mallick,et al. Partial uracil–DNA–glycosylase treatment for screening of ancient DNA , 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.
[24] Daniel L. Lindner,et al. Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies? , 2012 .
[25] Robert P. St.Onge,et al. Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples , 2010, Nucleic acids research.
[26] I. Weissman,et al. Index switching causes “spreading-of-signal” among multiplexed samples in Illumina HiSeq 4000 DNA sequencing , 2017, bioRxiv.
[27] John C Marioni,et al. Detection and removal of barcode swapping in single-cell RNA-seq data , 2017, Nature Communications.
[28] Anders Albrechtsen,et al. ANGSD: Analysis of Next Generation Sequencing Data , 2014, BMC Bioinformatics.
[29] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[30] Heng Li. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.
[31] Arcadi Navarro,et al. Great ape genetic diversity and population history , 2013, Nature.
[32] Albert J. Vilella,et al. Insights into hominid evolution from the gorilla genome sequence , 2012, Nature.
[33] Rickard Sandberg,et al. Computational correction of index switching in multiplexed sequencing libraries , 2018, Nature Methods.
[34] E. Hovig,et al. Sample-Index Misassignment Impacts Tumour Exome Sequencing , 2018, Scientific Reports.
[35] M. DePristo,et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.
[36] A. Albrechtsen,et al. Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data , 2018, Genetics.
[37] A. Meyerhans,et al. DNA recombination during PCR. , 1990, Nucleic acids research.
[38] Yossi Farjoun,et al. Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms , 2017, BMC Genomics.
[39] T. Günther,et al. The presence and impact of reference bias on population genomic studies of prehistoric human populations , 2018 .
[40] M. Hofreiter,et al. A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA , 2014, Science.
[41] Martin Kircher,et al. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform , 2011, Nucleic acids research.
[42] E. Wright,et al. Quality filtering of Illumina index reads mitigates sample cross-talk , 2016, BMC Genomics.
[43] Robert A. Edwards,et al. Quality control and preprocessing of metagenomic datasets , 2011, Bioinform..
[44] Eske Willerslev,et al. gargammel: a sequence simulator for ancient DNA , 2016, Bioinform..
[45] G. K. Sandve,et al. Exploiting antigen receptor information to quantify index switching in single-cell transcriptome sequencing experiments , 2018, PloS one.
[46] M. Thomas P. Gilbert,et al. Single‐tube library preparation for degraded DNA , 2017 .
[47] John G Kenny,et al. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling , 2016, BMC Genomics.
[48] Matthias Meyer,et al. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. , 2010, Cold Spring Harbor protocols.
[49] Peter H. Sudmant,et al. Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding , 2015, Science.
[50] T. Marquès-Bonet,et al. Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas , 2019, Current Biology.
[51] J. Wall,et al. Inconsistencies in Neanderthal Genomic DNA Sequences , 2007, PLoS genetics.
[52] D. Reich,et al. Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture , 2012, Genome research.
[53] M. Slatkin,et al. Distinguishing Recent Admixture from Ancestral Population Structure , 2017, Genome biology and evolution.