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Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1016/j.funeco.2012.06.003openalex-snapshot
Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?
inferredcites →https://doi.org/10.1038/nmeth.1251openalex-snapshot
Identification of genetic variants using bar-coded multiplexed sequencing
inferredcites →https://doi.org/10.1038/s41467-018-05083-xopenalex-snapshot
Detection and removal of barcode swapping in single-cell RNA-seq data
inferredcites →https://doi.org/10.1038/s41598-018-23563-4openalex-snapshot
Sample-Index Misassignment Impacts Tumour Exome Sequencing
inferredcites →https://doi.org/10.1038/s41598-018-24497-7openalex-snapshot
Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas
inferredcites →https://doi.org/10.1073/pnas.1318934111openalex-snapshot
Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btr026openalex-snapshot
Quality control and preprocessing of metagenomic datasets
inferredcites →https://doi.org/10.1093/bioinformatics/btu719openalex-snapshot
deML: robust demultiplexing of Illumina sequences using a likelihood-based approach
inferredcites →https://doi.org/10.1093/nar/23.11.2049openalex-snapshot
Template-switching during DNA synthesis byThermus aquaticusDNA polymerase I
inferredcites →https://doi.org/10.1093/nar/gkp1163openalex-snapshot
Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA
inferredcites →https://doi.org/10.1093/nar/gkq368openalex-snapshot
Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples
inferredcites →https://doi.org/10.1093/nar/gkr771openalex-snapshot
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
inferredcites →https://doi.org/10.1093/nar/gkv107openalex-snapshot
Accurate multiplexing and filtering for high-throughput amplicon-sequencing
inferredcites →https://doi.org/10.1098/rstb.2013.0624openalex-snapshot
Partial uracil–DNA–glycosylase treatment for screening of ancient DNA
inferredcites →https://doi.org/10.1101/125724openalex-snapshot
Index switching causes “spreading-of-signal” among multiplexed samples in Illumina HiSeq 4000 DNA sequencing
inferredcites →https://doi.org/10.1101/287821openalex-snapshot
Direct estimation of mutations in great apes reveals significant recent human slowdown in the yearly mutation rate
inferredcites →https://doi.org/10.1101/gr.128124.111openalex-snapshot
Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
inferredcites →https://doi.org/10.1101/pdb.prot5448openalex-snapshot
Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing
inferredcites →https://doi.org/10.1111/1755-0998.12713openalex-snapshot
A novel post hoc method for detecting index switching finds no evidence for increased switching on the Illumina HiSeq X
inferredcites →https://doi.org/10.1126/science.1188021openalex-snapshot
A Draft Sequence of the Neandertal Genome
inferredcites →https://doi.org/10.1126/science.1236573openalex-snapshot
A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA
inferredcites →https://doi.org/10.1126/science.aae0344openalex-snapshot
Long-read sequence assembly of the gorilla genome
inferredcites →https://doi.org/10.1186/s12859-014-0356-4openalex-snapshot
ANGSD: Analysis of Next Generation Sequencing Data
inferredcites →https://doi.org/10.1186/s12864-015-2194-9openalex-snapshot
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling
inferredcites →https://doi.org/10.1186/s12864-016-3217-xopenalex-snapshot
Quality filtering of Illumina index reads mitigates sample cross-talk
inferredcites →https://doi.org/10.1186/s13104-016-1900-2openalex-snapshot
AdapterRemoval v2: rapid adapter trimming, identification, and read merging
inferredcites →https://doi.org/10.1371/journal.pone.0094249openalex-snapshot
Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys
inferredcites →https://doi.org/10.1371/journal.pone.0120520openalex-snapshot
Strategies for Achieving High Sequencing Accuracy for Low Diversity Samples and Avoiding Sample Bleeding Using Illumina Platform
inferredcites →https://doi.org/10.1534/genetics.113.154138openalex-snapshot
Estimating Individual Admixture Proportions from Next Generation Sequencing Data
inferredcites →https://doi.org/10.1534/genetics.113.154740openalex-snapshot
Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.106670openalex-snapshot
Cross-contamination and strong mitonuclear discordance in Empria sawflies (Hymenoptera, Tenthredinidae) in the light of phylogenomic data
inferred← citeshttps://doi.org/10.1101/2022.08.04.502869openalex-snapshot
A two-decade microbial time series from a freshwater lake, introducing the limony and TYMEFLIES datasets
inferred← citeshttps://doi.org/10.1101/332346openalex-snapshot
Exploiting Index Cross-Talk to Modify Variant Calls
inferred← citeshttps://doi.org/10.1111/mec.14860openalex-snapshot
Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin
inferred← citeshttps://doi.org/10.1111/mec.15099openalex-snapshot
Killer whale genomes reveal a complex history of recurrent admixture and vicariance
inferred← citeshttps://doi.org/10.1186/s12711-018-0436-4openalex-snapshot
Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing
inferred← citeshttps://doi.org/10.1186/s12864-018-4703-0openalex-snapshot
Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms
inferred← citeshttps://doi.org/10.1371/journal.pone.0208484openalex-snapshot
Exploiting antigen receptor information to quantify index switching in single-cell transcriptome sequencing experiments
inferred← citeshttps://doi.org/10.1534/g3.119.400039openalex-snapshot
Whole Genome Sequencing and Progress Toward Full Inbreeding of the Mouse Collaborative Cross Population
inferred← citeshttps://doi.org/10.3389/fmicb.2020.578064openalex-snapshot
Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales
inferred← citeshttps://doi.org/10.3390/v13050922openalex-snapshot
Comparison of the Virome of Quarantined Sugarcane Varieties and the Virome of Grasses Growing near the Quarantine Station
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