Identifying biologically relevant differences between metagenomic communities Donovan H. Parks and Robert G. Beiko
نویسندگان
چکیده
منابع مشابه
Identifying biologically relevant differences between metagenomic communities
MOTIVATION Metagenomics is the study of genetic material recovered directly from environmental samples. Taxonomic and functional differences between metagenomic samples can highlight the influence of ecological factors on patterns of microbial life in a wide range of habitats. Statistical hypothesis tests can help us distinguish ecological influences from sampling artifacts, but knowledge of on...
متن کاملGenGIS: A geospatial information system for genomic data.
The increasing availability of genetic sequence data associated with explicit geographic and ecological information is offering new opportunities to study the processes that shape biodiversity. The generation and testing of hypotheses using these data sets requires effective tools for mathematical and visual analysis that can integrate digital maps, ecological data, and large genetic, genomic, ...
متن کاملRapid identification of high-confidence taxonomic assignments for metagenomic data
Determining the taxonomic lineage of DNA sequences is an important step in metagenomic analysis. Short DNA fragments from next-generation sequencing projects and microbes that lack close relatives in reference sequenced genome databases pose significant problems to taxonomic attribution methods. Our new classification algorithm, RITA (Rapid Identification of Taxonomic Assignments), uses the agr...
متن کاملGroopM: an automated tool for the recovery of population genomes from related metagenomes
Metagenomic binning methods that leverage differential population abundances in microbial communities (differential coverage) are emerging as a complementary approach to conventional composition-based binning. Here we introduce GroopM, an automated binning tool that primarily uses differential coverage to obtain high fidelity population genomes from related metagenomes. We demonstrate the effec...
متن کاملGenGIS 2: Geospatial Analysis of Traditional and Genetic Biodiversity, with New Gradient Algorithms and an Extensible Plugin Framework
GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gr...
متن کامل