Multiple comparative metagenomics using multiset k-mer counting
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Summary
This work demonstrates that analyzing metagenomes at the k-mer level is highly correlated with extremely precise de novo comparison techniques which rely on all-versus-all sequences alignment strategy or which are based on taxonomic profiling.
- Type
- article
- Published
- 2016-04-08
- Cited by
- 120
- References
- 47
- Access
- Open access
- OpenAlex
- https://openalex.org/W2339602899
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:7987311
Keywords
Metagenomics, Multiset, k-mer, Human Microbiome Project, Microbiome
References
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- Compareads: comparing huge metagenomic experiments
Cited by
- A resource-frugal probabilistic dictionary and applications in bioinformatics
- Novel computational techniques for mapping and classifying Next-Generation Sequencing data. (Nouvelles techniques informatiques pour la localisation et la classification de données de séquençage haut débit)
- A submarine volcanic eruption leads to a novel microbial habitat
- Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector
- Recentrifuge: robust comparative analysis and contamination removal for metagenomic data
- Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome
- MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota
- Assembly-free and alignment-free sample identification using genome skims
- Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms
- Metagenomic analysis of river microbial communities
- Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures
- Libra: Improved Partitioning Strategies for Massive Comparative Metagenomics Analysis
- Analyzing big datasets of genomic sequences: fast and scalable collection of k-mer statistics
- From reads to transcripts: de novo methods for the analysis of transcriptome second and third generation sequencing. (Des lectures aux transcrits: méthodes de novo pour l'analyse du séquençage des transcriptomes de deuxième et troisième génération)
- Precise and Parallel Pairwise Metagenomic Comparisons
- Streaming histogram sketching for rapid microbiome analytics
- A Data Adaptive Biological Sequence Representation for Supervised Learning
- City-wide metagenomics uncover antibiotic resistance reservoirs in urban beach and sewage waters
- APPLES: Fast Distance-based Phylogenetic Placement
- Libra: scalable k-mer–based tool for massive all-vs-all metagenome comparisons
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