ArticleBMC bioinformatics2015
MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 16 papers.
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16 citing papers in PubMed.
- Functional metatranscriptomics of the rhizosphere: towards an understanding of metabolic processes of the microbial carbon pump.FEMS microbiology ecology · 2026Article
- A Roadmap for Using Hybridisation Capture-Based Target Enrichment of Ancient Environmental DNA in Palaeoecology.Molecular ecology resources · 2026Review
- Genetic Potential for N₂O Metabolism in Tree Tissues: Insights From Nitrogen Cycling Gene Prevalence and nosZ Diversity Across Tree Species.Microbial ecology · 2026Article
- Activity and Abundance of Nitrous Oxide Reducing Bacteria in Platismatia glauca: An Epiphytic Lichen in the Boreal Spruce Forest.Environmental microbiology · 2026Article
- Review
- Methods, applications, and computational challenges in bait capture enrichment.Cell reports methods · 2025Review
- Probe Capture Enrichment Sequencing of amoA Genes Improves the Detection of Diverse Ammonia-Oxidising Archaeal and Bacterial Populations.Molecular ecology resources · 2025Article
- OLTA: Optimizing bait seLection for TArgeted sequencing.Bioinformatics (Oxford, England) · 2025Article
- Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.ISME communications · 2025Article
- Article
- ProbeTools: designing hybridization probes for targeted genomic sequencing of diverse and hypervariable viral taxa.BMC genomics · 2022Article
- Syotti: scalable bait design for DNA enrichment.Bioinformatics (Oxford, England) · 2022Article
- A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.Frontiers in genetics · 2019Review
- Design and evaluation of primers targeting genes encoding NO-forming nitrite reductases: implications for ecological inference of denitrifying communities.Scientific reports · 2016Article
- Erratum to: MetCap: A bioinformatics probe design pipeline for large-scale targeted metagenomics.BMC bioinformatics · 2016Article
- Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMassive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families.
resultsIn this study, we are presenting a web-based tool called MetCap that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated. To illustrate the advantage of a targeted metagenome approach, we have generated more than 400,000 probes that match more than 300,000 [corrected] publicly available sequences related to carbon degradation, and used these probes for target sequencing in a soil metagenome study. The results show high enrichment of target genes and a successful capturing of the majority of gene families. MetCap is freely available to users from: http://soilecology.biol.lu.se/metcap/ .
conclusionMetCap is facilitating probe-based target enrichment as an easy and efficient alternative tool compared to complex primer-based enrichment for large-scale investigations of metagenomes. Our results have shown efficient large-scale target enrichment through MetCap-designed probes for a soil metagenome. The web service is suitable for any targeted metagenomics project that aims to study several genes simultaneously. The novel bioinformatics approach taken by the web service will enable researchers in microbial ecology to tap into the vast diversity of microbial communities using targeted metagenomics as a cost-effective alternative to whole metagenome sequencing.
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