[HTML][HTML] KOMB: K-core based de novo characterization of copy number variation in microbiomes
Characterizing metagenomes via kmer-based, database-dependent taxonomic classification
has yielded key insights into underlying microbiome dynamics. However, novel approaches …
has yielded key insights into underlying microbiome dynamics. However, novel approaches …
KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome
The microbes present in the human gastrointestinal tract are regularly linked to human
health and disease outcomes. Thanks to technological and methodological advances in …
health and disease outcomes. Thanks to technological and methodological advances in …
[HTML][HTML] Quality control of microbiota metagenomics by k-mer analysis
F Plaza Onate, JM Batto, C Juste, J Fadlallah… - BMC genomics, 2015 - Springer
Background The biological and clinical consequences of the tight interactions between host
and microbiota are rapidly being unraveled by next generation sequencing technologies …
and microbiota are rapidly being unraveled by next generation sequencing technologies …
[HTML][HTML] Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases
While metagenomic sequencing has become the tool of preference to study host-associated
microbial communities, downstream analyses and clinical interpretation of microbiome data …
microbial communities, downstream analyses and clinical interpretation of microbiome data …
Metaviz: interactive statistical and visual analysis of metagenomic data
J Wagner, F Chelaru, J Kancherla… - Nucleic acids …, 2018 - academic.oup.com
Large studies profiling microbial communities and their association with healthy or disease
phenotypes are now commonplace. Processed data from many of these studies are publicly …
phenotypes are now commonplace. Processed data from many of these studies are publicly …
[HTML][HTML] Impact of host DNA and sequencing depth on the taxonomic resolution of whole metagenome sequencing for microbiome analysis
J Pereira-Marques, A Hout, RM Ferreira… - Frontiers in …, 2019 - frontiersin.org
The amount of host DNA poses a major challenge to metagenome analysis. However, there
is no guidance on the levels of host DNA, nor on the depth of sequencing needed to acquire …
is no guidance on the levels of host DNA, nor on the depth of sequencing needed to acquire …
[HTML][HTML] MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes
Background Metagenomes provide access to the taxonomic composition and functional
capabilities of microbial communities. Although metagenomic analysis methods exist for …
capabilities of microbial communities. Although metagenomic analysis methods exist for …
[HTML][HTML] Flexible metagenome analysis using the MGX framework
Background The characterization of microbial communities based on sequencing and
analysis of their genetic information has become a popular approach also referred to as …
analysis of their genetic information has become a popular approach also referred to as …
[HTML][HTML] Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis
Background A rapidly increasing flow of genomic data requires the development of efficient
methods for obtaining its compact representation. Feature extraction facilitates classification …
methods for obtaining its compact representation. Feature extraction facilitates classification …
[HTML][HTML] HirBin: high-resolution identification of differentially abundant functions in metagenomes
Background Gene-centric analysis of metagenomics data provides information about the
biochemical functions present in a microbiome under a certain condition. The ability to …
biochemical functions present in a microbiome under a certain condition. The ability to …