MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline

Background Microbial communities have become an important subject of research across multiple disciplines in recent years. These communities are often examined via shotgun metagenomic sequencing, a technology which can offer unique insights into the genomic content of a microbial community. Function...

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Vydáno v:BMC bioinformatics Ročník 21; číslo 1; s. 471 - 9
Hlavní autoři: Eng, Alexander, Verster, Adrian J., Borenstein, Elhanan
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 21.10.2020
BioMed Central Ltd
Springer Nature B.V
BMC
Témata:
Algorithms
Annotations
Antibiotics
Bioinformatics
Biomedical and Life Sciences
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer networks
Customization
Distributed computing
Distributed processing
Drug resistance
Functional annotation
Genes
Genomes
Humans
Integration
Life Sciences
Metagenomics
Metagenomics - methods
Microarrays
Microbial activity
Microbiota
Microorganisms
Pipeline
Pipeline design
Pipelines
Quality control
Sequence analysis
Software
Source code
Type 2 diabetes
Workflow software
Functional annotation
Metagenomics
Distributed computing
Pipeline
ISSN:1471-2105, 1471-2105
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Shrnutí:Background Microbial communities have become an important subject of research across multiple disciplines in recent years. These communities are often examined via shotgun metagenomic sequencing, a technology which can offer unique insights into the genomic content of a microbial community. Functional annotation of shotgun metagenomic data has become an increasingly popular method for identifying the aggregate functional capacities encoded by the community’s constituent microbes. Currently available metagenomic functional annotation pipelines, however, suffer from several shortcomings, including limited pipeline customization options, lack of standard raw sequence data pre-processing, and insufficient capabilities for integration with distributed computing systems. Results Here we introduce MetaLAFFA, a functional annotation pipeline designed to take unfiltered shotgun metagenomic data as input and generate functional profiles. MetaLAFFA is implemented as a Snakemake pipeline, which enables convenient integration with distributed computing clusters, allowing users to take full advantage of available computing resources. Default pipeline settings allow new users to run MetaLAFFA according to common practices while a Python module-based configuration system provides advanced users with a flexible interface for pipeline customization. MetaLAFFA also generates summary statistics for each step in the pipeline so that users can better understand pre-processing and annotation quality. Conclusions MetaLAFFA is a new end-to-end metagenomic functional annotation pipeline with distributed computing compatibility and flexible customization options. MetaLAFFA source code is available at https://github.com/borenstein-lab/MetaLAFFA and can be installed via Conda as described in the accompanying documentation.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-020-03815-9