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FALCON-meta: a method to infer metagenomic composition of ancient DNA

https://doi.org/10.1101/267179
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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A Mathematical Theory of Communication
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Endosymbiosis and Eukaryotic Cell Evolution
inferredcites →https://doi.org/10.1038/nature09710openalex-snapshot
Genetic history of an archaic hominin group from Denisova Cave in Siberia
inferredcites →https://doi.org/10.1038/nature21674openalex-snapshot
Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus
inferredcites →https://doi.org/10.1038/nbt.2676openalex-snapshot
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
inferredcites →https://doi.org/10.1038/nbt.3329openalex-snapshot
Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning
inferredcites →https://doi.org/10.1038/ng.2906openalex-snapshot
Pathogens and host immunity in the ancient human oral cavity
inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot
QIIME allows analysis of high-throughput community sequencing data
inferredcites →https://doi.org/10.1038/nprot.2014.063openalex-snapshot
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX
inferredcites →https://doi.org/10.1038/srep10203openalex-snapshot
An alignment-free method to find and visualise rearrangements between pairs of DNA sequences
inferredcites →https://doi.org/10.1038/srep23774openalex-snapshot
VIP: an integrated pipeline for metagenomics of virus identification and discovery
inferredcites →https://doi.org/10.1073/pnas.0704665104openalex-snapshot
Patterns of damage in genomic DNA sequences from a Neandertal
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/bts665openalex-snapshot
VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue
inferredcites →https://doi.org/10.1093/nar/29.23.4793openalex-snapshot
DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA
inferredcites →https://doi.org/10.1093/nar/gkr1124openalex-snapshot
GReEn: a tool for efficient compression of genome resequencing data
inferredcites →https://doi.org/10.1101/050559openalex-snapshot
MALT: Fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman
inferredcites →https://doi.org/10.1101/gr.171934.113openalex-snapshot
A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
inferredcites →https://doi.org/10.1101/gr.5969107openalex-snapshot
MEGAN analysis of metagenomic data
inferredcites →https://doi.org/10.1109/tit.2004.838101openalex-snapshot
The Similarity Metric
inferredcites →https://doi.org/10.1112/plms/s2-42.1.230openalex-snapshot
On Computable Numbers, with an Application to the Entscheidungsproblem
inferredcites →https://doi.org/10.1126/science.1224344openalex-snapshot
A High-Coverage Genome Sequence from an Archaic Denisovan Individual
inferredcites →https://doi.org/10.1126/science.aad2545openalex-snapshot
The 5300-year-old Helicobacter pylori genome of the Iceman
inferredcites →https://doi.org/10.1128/jvi.76.21.10608-10616.2002openalex-snapshot
Prevalence and Quantitation of Species C Adenovirus DNA in Human Mucosal Lymphocytes
inferredcites →https://doi.org/10.1186/1471-2164-13-178openalex-snapshot
Improving ancient DNA read mapping against modern reference genomes
inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot
Versatile and open software for comparing large genomes
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.1186/gb-2011-12-1-r1openalex-snapshot
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries
inferredcites →https://doi.org/10.1186/gb-2011-12-5-r51openalex-snapshot
Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths
inferredcites →https://doi.org/10.1371/journal.pone.0060307openalex-snapshot
Molecular Identification of Falciparum Malaria and Human Tuberculosis Co-Infections in Mummies from the Fayum Depression (Lower Egypt)

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/ece3.6082openalex-snapshot
Paleo‐metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA
inferred← citeshttps://doi.org/10.1007/978-3-030-23873-5_16openalex-snapshot
Visualization of Similar Primer and Adapter Sequences in Assembled Archaeal Genomes
inferred← citeshttps://doi.org/10.1007/978-3-031-99568-2_5openalex-snapshot
A Machine Learning Method for Authentication of Human Ancient Mitochondrial DNA
inferred← citeshttps://doi.org/10.1016/j.patrec.2018.05.026openalex-snapshot
Extended-alphabet finite-context models
inferred← citeshttps://doi.org/10.1016/j.softx.2020.100535openalex-snapshot
GTO: A toolkit to unify pipelines in genomic and proteomic research
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab437openalex-snapshot
RENANO: a REference-based compressor for NANOpore FASTQ files
inferred← citeshttps://doi.org/10.1093/bioinformatics/btag155openalex-snapshot
FALCON2: compression-based metagenomic classification of ancient viruses
inferred← citeshttps://doi.org/10.1101/2025.11.07.687203openalex-snapshot
Metagenomic classification of ancient viruses
inferred← citeshttps://doi.org/10.23919/eusipco.2018.8553297openalex-snapshot
Metagenomic composition analysis of sedimentary ancient DNA from the Isle of Wight
inferred← citeshttps://doi.org/10.3390/e20060393openalex-snapshot
Comparison of Compression-Based Measures with Application to the Evolution of Primate Genomes
inferred← citeshttps://doi.org/10.3390/genes9090445openalex-snapshot
Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard
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