Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.
Nucleic Acids Res
; 47(10): e57, 2019 06 04.
Article
em En
| MEDLINE
| ID: mdl-30838416
ABSTRACT
Shotgun metagenomics is a powerful, high-resolution technique enabling the study of microbial communities in situ. However, species-level resolution is only achieved after a process of 'binning' where contigs predicted to originate from the same genome are clustered. Such culture-independent sequencing frequently unearths novel microbes, and so various methods have been devised for reference-free binning. As novel microbiomes of increasing complexity are explored, sometimes associated with non-model hosts, robust automated binning methods are required. Existing methods struggle with eukaryotic contamination and cannot handle highly complex single metagenomes. We therefore developed an automated binning pipeline, termed 'Autometa', to address these issues. This command-line application integrates sequence homology, nucleotide composition, coverage and the presence of single-copy marker genes to separate microbial genomes from non-model host genomes and other eukaryotic contaminants, before deconvoluting individual genomes from single metagenomes. The method is able to effectively separate over 1000 genomes from a metagenome, allowing the study of previously intractably complex environments at the level of single species. Autometa is freely available at https//bitbucket.org/jason_c_kwan/autometa and as a docker image at https//hub.docker.com/r/jasonkwan/autometa under the GNU Affero General Public License 3 (AGPL 3).
Texto completo:
1
Bases de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Biologia Computacional
/
Metagenoma
/
Metagenômica
/
Genoma Microbiano
Tipo de estudo:
Prognostic_studies
Limite:
Animals
/
Humans
Idioma:
En
Revista:
Nucleic Acids Res
Ano de publicação:
2019
Tipo de documento:
Article
País de afiliação:
Estados Unidos