PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly
出版年份 2021 全文链接
标题
PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly
作者
关键词
-
出版物
PeerJ
Volume 9, Issue -, Pages e11845
出版商
PeerJ
发表日期
2021-07-27
DOI
10.7717/peerj.11845
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Reconstruction of ancient microbial genomes from the human gut
- (2021) Marsha C. Wibowo et al. NATURE
- SciPy 1.0: fundamental algorithms for scientific computing in Python
- (2020) Pauli Virtanen et al. NATURE METHODS
- Dental calculus as a tool to study the evolution of the mammalian oral microbiome
- (2020) Jaelle C Brealey et al. MOLECULAR BIOLOGY AND EVOLUTION
- CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content
- (2020) Maxime Borry et al. PeerJ
- Thanatomicrobiome and epinecrotic community signatures for estimation of post-mortem time interval in human cadaver
- (2020) Hirak Ranjan Dash et al. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
- Microbial succession from a subsequent secondary death event following mass mortality
- (2020) Lindsay Harrison et al. BMC MICROBIOLOGY
- Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
- (2019) Edoardo Pasolli et al. CELL
- Taxonomic features and comparisons of the gut microbiome from two edible fungus-farming termites (Macrotermes falciger; M. natalensis) harvested in the Vhembe district of Limpopo, South Africa
- (2019) Stephanie L. Schnorr et al. BMC MICROBIOLOGY
- A genetic analysis of the Gibraltar Neanderthals
- (2019) Lukas Bokelmann et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe
- (2019) Stéphane Peyrégne et al. Science Advances
- The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations
- (2019) Adrian Tett et al. Cell Host & Microbe
- Antimicrobial Resistance in Bacteria: Mechanisms, Evolution, and Persistence
- (2019) Eirini Christaki et al. JOURNAL OF MOLECULAR EVOLUTION
- Differential preservation of endogenous human and microbial DNA in dental calculus and dentin
- (2018) Allison E. Mann et al. Scientific Reports
- metaSPAdes: a new versatile metagenomic assembler
- (2017) Sergey Nurk et al. GENOME RESEARCH
- Influence of diet on the gut microbiome and implications for human health
- (2017) Rasnik K. Singh et al. Journal of Translational Medicine
- Improving ancient DNA genome assembly
- (2017) Alexander Seitz et al. PeerJ
- Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum
- (2017) Henrik B. Hansen et al. PLoS One
- gargammel: a sequence simulator for ancient DNA
- (2016) Gabriel Renaud et al. BIOINFORMATICS
- Insights into human evolution from ancient and contemporary microbiome studies
- (2016) Stephanie L Schnorr et al. CURRENT OPINION IN GENETICS & DEVELOPMENT
- Subsistence strategies in traditional societies distinguish gut microbiomes
- (2015) Alexandra J. Obregon-Tito et al. Nature Communications
- MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
- (2015) Dongwan D. Kang et al. PeerJ
- Prokka: rapid prokaryotic genome annotation
- (2014) T. Seemann BIOINFORMATICS
- Pathogens and host immunity in the ancient human oral cavity
- (2014) Christina Warinner et al. NATURE GENETICS
- Partial uracil-DNA-glycosylase treatment for screening of ancient DNA
- (2014) N. Rohland et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal
- (2014) Pontus Skoglund et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Gut microbiome of the Hadza hunter-gatherers
- (2014) Stephanie L. Schnorr et al. Nature Communications
- mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
- (2013) Hákon Jónsson et al. BIOINFORMATICS
- Ancient DNA Damage
- (2013) J. Dabney et al. Cold Spring Harbor Perspectives in Biology
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- A High-Coverage Genome Sequence from an Archaic Denisovan Individual
- (2012) M. Meyer et al. SCIENCE
- mapDamage: testing for damage patterns in ancient DNA sequences
- (2011) Aurelien Ginolhac et al. BIOINFORMATICS
- Antibiotic resistance is ancient
- (2011) Vanessa M. D’Costa et al. NATURE
- How to apply de Bruijn graphs to genome assembly
- (2011) Phillip E C Compeau et al. NATURE BIOTECHNOLOGY
- FragGeneScan: predicting genes in short and error-prone reads
- (2010) Mina Rho et al. NUCLEIC ACIDS RESEARCH
- 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
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