Filters








39 Hits in 1.9 sec

gargammel: a sequence simulator for ancient DNA

Gabriel Renaud, Kristian Hanghøj, Eske Willerslev, Ludovic Orlando
2016 Bioinformatics  
Acknowledgments We thank Weichun Huang and all members of the Paleomix group at the Centre for GeoGenetics for fruitful discussions.  ...  Funding This work was supported by the Danish Council for Independent Research, Natural Sciences (4002-00152B); the Danish National Research Foundation  ...  The results presented in the Supplementary Results show a high consistency between observed and simulated distributions to show the applicability of gargammel as a sequence simulator for aDNA.  ... 
doi:10.1093/bioinformatics/btw670 pmid:27794556 pmcid:PMC5408798 fatcat:nj6tfkofh5dg3osvotulrjavdq

DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage

Kristian Hanghøj, Gabriel Renaud, Anders Albrechtsen, Ludovic Orlando
2019 GigaScience  
Recent computational advances in ancient DNA research have opened access to the detection of ancient DNA methylation footprints at the genome-wide scale.  ...  However, this approach overlooks a number of confounding factors, including the presence of sequencing errors and true variants.  ...  Acknowledgments We thank the AGES Group members for fruitful discussions and 2 reviewers for constructive feedback.  ... 
doi:10.1093/gigascience/giz025 pmid:31004132 pmcid:PMC6474913 fatcat:oyjmphtgrnf5vlr22gr6vezyba

Assessing alignment-based taxonomic classification of ancient microbial DNA

Raphael Eisenhofer, Laura Susan Weyrich
2019 PeerJ  
We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification.  ...  Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying  ...  A total of 29 oral and environmental genomes were used as input for Gargammel (Renaud et al., 2017) to generate simulated ancient metagenomes of 1.5 million fragmented sequences each.  ... 
doi:10.7717/peerj.6594 pmid:30886779 pmcid:PMC6420809 fatcat:icvhdwijgzbi3omo6ggu5iizqy

Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis [article]

Umit Akkose, Ogun Adebali
2022 bioRxiv   pre-print
It also allows the use of input DNA sequencing to correct the bias due to the copy number variations in the genome.  ...  Boquila uses standard file formats for input and output data, and it can be easily integrated into any workflow for high-throughput sequencing applications.  ...  Gargammel, ancient DNA sequencing simulator, uses sequencing errors and quality profiles can model base compositions. It can mimic UV damage by adding deamination.  ... 
doi:10.1101/2022.03.29.486262 fatcat:dqwhcwapvfaj3jnbjt3hjwcxwe

PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly

Maxime Borry, Alexander Hübner, Adam B. Rohrlach, Christina Warinner
2021 PeerJ  
The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences  ...  Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing  ...  ACKNOWLEDGEMENTS We thank Nigel Bean and Jonathon Tuke for extremely useful discussions. ADDITIONAL INFORMATION AND DECLARATIONS  ... 
doi:10.7717/peerj.11845 fatcat:mrlsgow4onhz3fv4z6s32yxhmq

PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly [article]

Maxime Borry, Alexander Huebner, Adam B Rohrlach, Christina G Warinner
2021 bioRxiv   pre-print
The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences  ...  Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences.  ...  INTRODUCTION PyDamage takes alignment files of reads (in SAM, BAM, or CRAM format) mapped against reference sequences (i.e., contigs, a MAG, a genome, or any other reference sequences of DNA).  ... 
doi:10.1101/2021.03.24.436838 fatcat:4v6rwt2nsnbqpgwyiotp2i5ba4

ARIADNA: machine learning method for ancient DNA variant discovery

Joseph K Kawash, Sean D Smith, Spyros Karaiskos, Andrey Grigoriev
2018 DNA Research  
To address these problems, we present ARIADNA (ARtificial Intelligence for Ancient DNA), a novel approach based on machine learning techniques, using specific aDNA characteristics as features to yield  ...  Ancient DNA (aDNA) studies often rely on standard methods of mutation calling, optimized for high-quality contemporary DNA but not for excessive contamination, time-or environmentrelated damage of aDNA  ...  Here, we introduce ARIADNA (ARtificial Intelligence for Ancient DNA), a novel approach for detecting single-nucleotide variants (SNVs) in aDNA samples.  ... 
doi:10.1093/dnares/dsy029 pmid:30215675 fatcat:imajoutqtbb2zobiqv733el7ia

Metagenomic analysis of coprolites from three Late Pleistocene megaherbivores from the Southwestern United States [article]

Tomos O. Prys-Jones, Tara N. Furstenau, Andrew J. Abraham, Isaac N. Shaffer, Colin J. Sobek, Jordyn R. Upton, Samantha N. Hershauer, Kelvin Wong, Marirosa Molina, Sebastian Menke, Jim I. Mead, Christopher H. Ebert (+5 others)
2022 bioRxiv   pre-print
The novel metagenomic classifier MTSv, parameterized for studies of aDNA, was used to assign bacterial taxa to sequencing reads.  ...  was performed on ancient DNA (aDNA) extracted from coprolites of the Columbian mammoth (Mammuthus Columbi), Shasta ground sloth (Nothrotheriops shastensis) and paleontological bison (Bison sp.) collected  ...  Based on the gargammel simulations the preferred MTSv parameters for the classification of ancient DNA was a k-mer query length of 36 bp, 3 edits permitted between a given read and reference, and the alignment  ... 
doi:10.1101/2022.05.06.490351 fatcat:tseadpkvd5hfbfgml2vzdcfkgy

Reconstructing mitochondrial genomes from ancient DNA through iterative mapping: an evaluation of software, parameters, and bait reference [article]

Michael Vincent Westbury, Eline D Lorenzen
2021 bioRxiv   pre-print
However, most are not suitable for divergent, extinct species, due to the requirement of a reference mitogenome from a conspecific or close relative, and relatively high-quality DNA. (2) Iterative mapping  ...  The same was observed for the number of incorrectly inserted bp. In contrast, the total sequence length was lower.  ...  Discussion We investigated the influence of mapping software, parameters, and bait reference sequence on reconstructing mitogenomes from ancient DNA through iterative mapping, providing a reference for  ... 
doi:10.1101/2021.12.16.472923 fatcat:kb2phtispbgnra5fg6wl6z4f2m

Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research [article]

Irina Marie Velsko, Laurent A. F. Frantz, Alexander Herbig, Greger Larson, Christina Warinner
2018 biorxiv/medrxiv   pre-print
Ancient DNA damage resulted in minimal differences in species detection and relative abundance between simulated ancient and modern datasets for most programs.  ...  Using a set of in silico-generated metagenomic datasets we investigated how the addition of ancient DNA (aDNA) damage patterns influences microbial taxonomic assignment by five widely-used profilers: QIIME  ...  .), the United States National Science Foundation (BCS-1516633 to C.W. and BCS- We thank Louise Loe for access to the Radcliffe Infirmary burial ground collection. We thank James A.  ... 
doi:10.1101/260042 fatcat:esd42xruvbaujhijwgolgbdtxa

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

Rui Martiniano, Erik Garrison, Eppie R Jones, Andrea Manica, Richard Durbin
2020 Genome Biology  
During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations.  ...  We use vg to align simulated and real aDNA samples to a variation graph containing 1000 Genome Project variants and compare with the same data aligned with bwa to the human linear reference genome.  ...  Acknowledgements We thank Cosimo Posth and Stephan Schiffels for assistance in obtaining raw sequence data, Christiana Lyn Scheib and Toomas Kivisild for sharing their results on reference bias in ancient  ... 
doi:10.1186/s13059-020-02160-7 pmid:32943086 pmcid:PMC7499850 fatcat:flo2e7q7kzcnfpq6bxg22j4uca

Removing reference bias in ancient DNA data analysis by mapping to a sequence variation graph [article]

Rui Martiniano, Erik Garrison, Eppie R Jones, Andrea Manica, Richard Durbin
2019 bioRxiv   pre-print
During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations.  ...  Here, we evaluate the use of variation graph software vg to avoid reference bias for ancient DNA.  ...  Acknowledgements We thank Cosimo Posth and Stephan Schiffels for assistance in obtaining raw sequence data, Christiana Lyn Scheib and Toomas Kivisild for sharing their results on reference bias in ancient  ... 
doi:10.1101/782755 fatcat:dyniq4jr7na35h5ena6to42suy

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

Ulrike Taron, Moritz Lell, Axel Barlow, Johanna Paijmans
2018 Genes  
In this paper, we present 'TAPAS', (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence  ...  The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences.  ...  We thank Kirstin Henneberger (University of Potsdam, Potsdam, Germany) for performing the lab work for the linsang sample.  ... 
doi:10.3390/genes9030157 pmid:29533977 pmcid:PMC5867878 fatcat:t723ztajangpxfdmms2caxu5re

Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research

Irina M. Velsko, Laurent A. F. Frantz, Alexander Herbig, Greger Larson, Christina Warinner, Thomas J. Sharpton
2018 mSystems  
The addition of ancient DNA damage resulted in minimal differences in species detection and relative abundance between simulated ancient and modern data sets for most programs.  ...  Using a set of in silico-generated metagenomic data sets, we investigated how the addition of ancient DNA (aDNA) damage patterns influences microbial taxonomic assignment by five widely used profilers:  ...  .), the United States National Science Foundation (BCS-1516633 to C.W. and BCS- We thank Louise Loe for access to the Radcliffe Infirmary burial ground collection. We thank James A.  ... 
doi:10.1128/msystems.00080-18 pmid:30035235 pmcid:PMC6050634 fatcat:mfa7ok3wifhm5noknmbo3ncmcy

HOPS: automated detection and authentication of pathogen DNA in archaeological remains

Ron Hübler, Felix M. Key, Christina Warinner, Kirsten I. Bos, Johannes Krause, Alexander Herbig
2019 Genome Biology  
Here, we present HOPS (Heuristic Operations for Pathogen Screening), an automated bacterial screening pipeline for ancient DNA sequences that provides detailed information on species identification and  ...  HOPS is a versatile tool for high-throughput screening of DNA from archaeological material to identify candidates for genome-level analyses.  ...  Acknowledgements We thank the Department of Archaeogenetics of the Max Planck Institute for the Science of Human History and Julian Susat for beta testing and helpful discussions.  ... 
doi:10.1186/s13059-019-1903-0 pmid:31842945 pmcid:PMC6913047 fatcat:qakuvfssnbedzlxp7sochwex2q
« Previous Showing results 1 — 15 out of 39 results