MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline
Abstract 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....
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2020-10-01
|
| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-020-03815-9 |
| _version_ | 1828543416975228928 |
|---|---|
| author | Alexander Eng Adrian J. Verster Elhanan Borenstein |
| author_facet | Alexander Eng Adrian J. Verster Elhanan Borenstein |
| author_sort | Alexander Eng |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-12T02:13:31Z |
| format | Article |
| id | doaj.art-c1239bd2f6e04e94856fcf733dbadeb9 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-12T02:13:31Z |
| publishDate | 2020-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-c1239bd2f6e04e94856fcf733dbadeb92022-12-22T00:41:51ZengBMCBMC Bioinformatics1471-21052020-10-012111910.1186/s12859-020-03815-9MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipelineAlexander Eng0Adrian J. Verster1Elhanan Borenstein2Department of Genome Sciences, University of WashingtonDepartment of Genome Sciences, University of WashingtonBlavatnik School of Computer Science, Tel Aviv UniversityAbstract 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.http://link.springer.com/article/10.1186/s12859-020-03815-9MetagenomicsFunctional annotationPipelineDistributed computing |
| spellingShingle | Alexander Eng Adrian J. Verster Elhanan Borenstein MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline BMC Bioinformatics Metagenomics Functional annotation Pipeline Distributed computing |
| title | MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline |
| title_full | MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline |
| title_fullStr | MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline |
| title_full_unstemmed | MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline |
| title_short | MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline |
| title_sort | metalaffa a flexible end to end distributed computing compatible metagenomic functional annotation pipeline |
| topic | Metagenomics Functional annotation Pipeline Distributed computing |
| url | http://link.springer.com/article/10.1186/s12859-020-03815-9 |
| work_keys_str_mv | AT alexandereng metalaffaaflexibleendtoenddistributedcomputingcompatiblemetagenomicfunctionalannotationpipeline AT adrianjverster metalaffaaflexibleendtoenddistributedcomputingcompatiblemetagenomicfunctionalannotationpipeline AT elhananborenstein metalaffaaflexibleendtoenddistributedcomputingcompatiblemetagenomicfunctionalannotationpipeline |