MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics

作者：Sandeep Kushwaha, Lokeshwaran Manoharan, Tejashwari Meerupati, Katarina Hedlund, Dag Ahrén · 发表于：BMC Bioinformatics · 年份：2015 · DOI：10.1186/s12859-015-0501-8 · 被引用次数：43 · 研究领域：Genomics and Phylogenetic Studies、Microbial Community Ecology and Physiology、Gene expression and cancer classification

BACKGROUND: Massive 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. RESULTS: In 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 capturin...