Consistency of metagenomic assignment programs in simulated and real data
[Backgroun] Metagenomics is the genomic study of uncultured environmental samples, which has been greatly facilitated by the advent of shotgun-sequencing technologies. One of the main focuses of metagenomics is the discovery of previously uncultured microorganisms, which makes the assignment of sequences to a particular taxon a challenge and a crucial step. Recently, several methods have been developed to perform this task, based on different methodologies such as sequence composition or sequence similarity. The sequence composition methods have the ability to completely assign the whole dataset. However, their use in metagenomics and the study of their performance with real data is limited. In this work, we assess the consistency of three different methods (BLAST + Lowest Common Ancestor, Phymm, and Naïve Bayesian Classifier) in assigning real and simulated sequence reads.
Main Authors: | García-Etxebarria, Koldo, Garcia-Garcerà, Marc, Calafell, Francesc |
---|---|
Other Authors: | Ministerio de Ciencia e Innovación (España) |
Format: | artículo biblioteca |
Published: |
BioMed Central
2014-03-28
|
Online Access: | http://hdl.handle.net/10261/95685 http://dx.doi.org/10.13039/501100004837 |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
-
A New Method for Extracting Skin Microbes Allows Metagenomic Analysis of Whole-Deep Skin
by: Garcia-Garcerà, Marc, et al.
Published: (2013-09-20) -
No Major Host Genetic Risk Factor Contributed to A(H1N1)2009 Influenza Severity
by: García-Etxebarria, Koldo, et al.
Published: (2015-09-17) -
Staphylococcus prevails in the skin microbiota of long-term immunodeficient mice
by: Garcia-Garcerà, Marc, et al.
Published: (2012-08) -
Increase in taxonomic assignment efficiency of viral reads in metagenomic studies
by: François, Sarah, et al. -
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
by: Cantalapiedra, Carlos P, et al.
Published: (2021-12)