What technique required entirely new toolsets for assembly and functional analysis?
Answer
Whole-genome shotgun metagenomics
The field experienced a significant conceptual and technical leap when moving past targeted 16S rRNA gene sequencing to whole-genome shotgun metagenomics. Shotgun sequencing involves sequencing all the DNA present in a sample, rather than focusing on one marker gene. This generated data that answered the question of 'what they can do' rather than just 'who is there.' Consequently, this data required entirely new computational toolsets capable of complex operations like sequence assembly, identifying potential genes (gene prediction), and performing comprehensive functional analysis, tasks that 16S pipelines were not designed to handle.
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