Lesson plan
PICRUSt
PICRUSt is a bioinformatics software package. The name is an abbreviation for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. The tool serves in the field of metagenomic analysis where it allows inference of the functional profile of a microbial community based on marker gene survey along one or more samples. In essence, PICRUSt takes a user supplied operational taxonomic unit table (typically referred to as an OTU table), representing the marker gene sequences (most commonly a 16S cluster) accompanied with its relative abundance in each of the samples. The output of PICRUSt is a sample by functional-gene-count matrix, telling the count of each functional-gene in each of the samples surveyed. The ability of PICRUSt to estimate the functional-gene profile for a given sample relies on a set of known sequenced genomes. This could also be thought of as an automated alternative to manually researching the gene families likely to be present in organisms whose sequences are found in a 16S ribosomal RNA amplicon library. The below description corresponds to the original version of PICRUSt, but a major update to this tool is currently being developed.
Article summary
PICRUSt is a bioinformatics software package. The name is an abbreviation for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. The tool serves in the field of metagenomic analysis where it allows inference of the functional profile of a microbial community based on marker gene survey along one or more samples. In essence, PICRUSt takes a user supplied operational taxonomic unit table (typically referred to as an OTU table), representing the marker gene sequences (most commonly a 16S cluster) accompanied with its relative abundance in each of the samples. The output of PICRUSt is a sample by functional-gene-count matrix, telling the count of each functional-gene in each of the samples surveyed. The ability of PICRUSt to estimate the functional-gene profile for a given sample relies on a set of known sequenced genomes. This could also be thought of as an automated alternative to manually researching the gene families likely to be present in organisms whose sequences are found in a 16S ribosomal RNA amplicon library. The below description corresponds to the original version of PICRUSt, but a major update to this tool is currently being developed.
Key claims
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Discussion questions
- Summarise the article in your own words. Which single claim would you verify first, and why?
- Which claim in this article is most likely to be revised as the sources update? How would you check its current status?
- If two sources disagreed about one of these facts, what would you need in order to trust one over the other?
Bibliography
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Key claims and bibliography are generated from the same tracked claims and sources as the article page.