FunFrame is a pipeline for the ecological analysis of protein-coding genes using targeted metagemomic DNA sequencing. Briefly, FunFrame reads targeted metagenomic sequence data from multiple biological samples, identifies and repairs likely homopolymer read errors, performs ecological analysis on the de-noised sequences, and produces reports describing the microbial communities at each biological sample. The input metagenomic sequence data is typically the product of PCR amplification using universal primers for a specific protein-coding gene prefixed with adaptor and barcode extensions, and read with next-generation pyrosequencing technology.
- R package
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FunFrame: functional gene ecological analysis pipeline
David Weisman, Michie Yasuda and Jennifer L. Bowen
Bioinformatics (2013) 29 (9): 1212-1214.