Recovering and annotating bacterial genomes from metagenomes involves a series of complex computational tools that are often difficult to use for researches without a specialistic bioinformatic background. In this chapter we review all the steps that lead from raw reads to a collection of quality-controlled, functionally annotated bacterial genomes and propose a working protocol using state-of-the-art, open source software tools.

Albanese, D.; Donati, C. (2021). Genome recovery, functional profiling, and taxonomic classification from metagenomes. In: Bacterial Pangenomics: Methods and Protocols (editor(s) Mengoni, A.; Bacci, G.; Fondi, M.). Berlin ... [et al.]: Springer. (METHODS IN MOLECULAR BIOLOGY): 153-172. ISBN: 9781071610985 doi: 10.1007/978-1-0716-1099-2_10. handle: http://hdl.handle.net/10449/69768

Genome recovery, functional profiling, and taxonomic classification from metagenomes

Albanese, Davide
Primo
;
Donati, Claudio
Ultimo
2021-01-01

Abstract

Recovering and annotating bacterial genomes from metagenomes involves a series of complex computational tools that are often difficult to use for researches without a specialistic bioinformatic background. In this chapter we review all the steps that lead from raw reads to a collection of quality-controlled, functionally annotated bacterial genomes and propose a working protocol using state-of-the-art, open source software tools.
Next Generation Sequencing
Metagenomics
Assembly
Coassembly
MAG
Metagenome-assembled genome
Binning
Dereplication
Taxonomic classification
Functional annotation
Quality control
Settore BIO/19 - MICROBIOLOGIA GENERALE
2021
9781071610985
Albanese, D.; Donati, C. (2021). Genome recovery, functional profiling, and taxonomic classification from metagenomes. In: Bacterial Pangenomics: Methods and Protocols (editor(s) Mengoni, A.; Bacci, G.; Fondi, M.). Berlin ... [et al.]: Springer. (METHODS IN MOLECULAR BIOLOGY): 153-172. ISBN: 9781071610985 doi: 10.1007/978-1-0716-1099-2_10. handle: http://hdl.handle.net/10449/69768
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