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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.
(Kushwaha et al., 2015) MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics. BMC Bioinformatics.