Background Next-Generation-Sequencing (NGS) enables detection of microorganisms present in biological and other matrices of various origin and nature, allowing not only the identification of known phyla and strains but also the discovery of novel ones. The large amount of metagenomic shotgun data ...
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420–1428 (2012). Article CAS PubMed Google Scholar Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. ...
To further characterize the honey DNA metagenomic data of the analysed samples, we identified which organisms could be considered equally abundant across samples. A total of ten organisms were detected to be equally abundant (CV% < 10.0) (Table3), all belonged to Bacteria. Among them, the...
RESEARCH ARTICLEShotgun Metagenomic Sequencing RevealsFunctional Genes and Microbiome Associatedwith Bovine Digital DermatitisMartin Zinicola, Hazel Higgins, Svetlana Lima, Vinicius Machado, Charles Guard,Rodrigo Bicalho*Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New Yo...
we developed a tool that enables fungal taxonomic and functional profiling from shotgun metagenomic sequence data [11]. Another reason for this knowledge gap may lie in the sequencing approach that has been so far used to access the composition of the fungal microbiome. Indeed, similar to the ...
Microbiome Colorectal cancer Metagenomic shotgun sequencing Random forests 1. Introduction Human microbial community is an aggregate of bacteria, archaea, viruses, plasmids, eukaryotes, etc. that reside on or within human body sites. According to the Human Microbiome Project, these microorganisms are ten...
Metagenomic raw sequencing data have been deposited in SRA database with BioProject ID PRJNA1065874. Raw data can be accessed here: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1065874Abbreviations CG: Chronic gastritis FFQ: Food Frequency Questionnaire GCA: Gastric Cancer IM: Internal Metaplasia...
为什么说shotgun metagenomic sequencing is generally not deep enough to detect rare species in complex...
All shotgun metagenomic sequencing data can be also found at the MG-RAST server (for the strain P50: http://www.mg-rast.org/ mgmain.html?mgpage=overview&metagenome=mgm4767611.3; strain QB: http://www.mg-rast.org/ mgmain.html?mgpage=overview&metagenome=mgm4754041.3). The annotation ...
Hence, metagenomic data deliver knowledge on the taxonomic composition of the ecosystem under study but also on functional genes in the sample, an information that is not retrievable with 16S rRNA gene sequencing. On the other hand, shotgun metagenomics requires higher coverage than metataxonomics...