An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs
Here, we describe MetaErg, a standalone and fully automated metagenome and metaproteome annotation pipeline. Annotation of metagenomes is challenging. First, metagenomes contain sequence data of many organisms from all domains of life. Second, many of these are from understudied lineages, encoding g...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-10-01
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| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.00999/full |
| _version_ | 1811193487600648192 |
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| author | Xiaoli Dong Marc Strous |
| author_facet | Xiaoli Dong Marc Strous |
| author_sort | Xiaoli Dong |
| collection | DOAJ |
| description | Here, we describe MetaErg, a standalone and fully automated metagenome and metaproteome annotation pipeline. Annotation of metagenomes is challenging. First, metagenomes contain sequence data of many organisms from all domains of life. Second, many of these are from understudied lineages, encoding genes with low similarity to experimentally validated reference genes. Third, assembly and binning are not perfect, sometimes resulting in artifactual hybrid contigs or genomes. To address these challenges, MetaErg provides graphical summaries of annotation outcomes, both for the complete metagenome and for individual metagenome-assembled genomes (MAGs). It performs a comprehensive annotation of each gene, including taxonomic classification, enabling functional inferences despite low similarity to reference genes, as well as detection of potential assembly or binning artifacts. When provided with metaproteome information, it visualizes gene and pathway activity using sequencing coverage and proteomic spectral counts, respectively. For visualization, MetaErg provides an HTML interface, bringing all annotation results together, and producing sortable and searchable tables, collapsible trees, and other graphic representations enabling intuitive navigation of complex data. MetaErg, implemented in Perl, HTML, and JavaScript, is a fully open source application, distributed under Academic Free License at https://github.com/xiaoli-dong/metaerg. MetaErg is also available as a docker image at https://hub.docker.com/r/xiaolidong/docker-metaerg. |
| first_indexed | 2024-04-12T00:09:37Z |
| format | Article |
| id | doaj.art-7eaf7ec9ad5c43968f660c027e06f0f6 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-12T00:09:37Z |
| publishDate | 2019-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-7eaf7ec9ad5c43968f660c027e06f0f62022-12-22T03:56:00ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-10-011010.3389/fgene.2019.00999464890An Integrated Pipeline for Annotation and Visualization of Metagenomic ContigsXiaoli DongMarc StrousHere, we describe MetaErg, a standalone and fully automated metagenome and metaproteome annotation pipeline. Annotation of metagenomes is challenging. First, metagenomes contain sequence data of many organisms from all domains of life. Second, many of these are from understudied lineages, encoding genes with low similarity to experimentally validated reference genes. Third, assembly and binning are not perfect, sometimes resulting in artifactual hybrid contigs or genomes. To address these challenges, MetaErg provides graphical summaries of annotation outcomes, both for the complete metagenome and for individual metagenome-assembled genomes (MAGs). It performs a comprehensive annotation of each gene, including taxonomic classification, enabling functional inferences despite low similarity to reference genes, as well as detection of potential assembly or binning artifacts. When provided with metaproteome information, it visualizes gene and pathway activity using sequencing coverage and proteomic spectral counts, respectively. For visualization, MetaErg provides an HTML interface, bringing all annotation results together, and producing sortable and searchable tables, collapsible trees, and other graphic representations enabling intuitive navigation of complex data. MetaErg, implemented in Perl, HTML, and JavaScript, is a fully open source application, distributed under Academic Free License at https://github.com/xiaoli-dong/metaerg. MetaErg is also available as a docker image at https://hub.docker.com/r/xiaolidong/docker-metaerg.https://www.frontiersin.org/article/10.3389/fgene.2019.00999/fullmetagenomicsmetaproteomicsbioinformaticsgene predictionfunctional annotationtaxonomic classification |
| spellingShingle | Xiaoli Dong Marc Strous An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs Frontiers in Genetics metagenomics metaproteomics bioinformatics gene prediction functional annotation taxonomic classification |
| title | An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs |
| title_full | An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs |
| title_fullStr | An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs |
| title_full_unstemmed | An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs |
| title_short | An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs |
| title_sort | integrated pipeline for annotation and visualization of metagenomic contigs |
| topic | metagenomics metaproteomics bioinformatics gene prediction functional annotation taxonomic classification |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.00999/full |
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