QIIME (an abbreviation for ''Quantitative Insights Into Microbial Ecology'') is a bioinformatic pipeline designated for the task of analysing

microbial A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...

communities A community is a Level of analysis, social unit (a group of living things) with commonality such as place (geography), place, Norm (social), norms, religion, values, Convention (norm), customs, or Identity (social science), identity. Communiti ...

that were sampled through

marker gene In biology, a marker gene may have several meanings. In nuclear biology and molecular biology, a marker gene is a gene used to determine if a nucleic acid sequence has been successfully inserted into an organism's DNA. In particular, there are tw ...

(e.g. 16S or 18S rRNA genes)

amplicon In molecular biology, an amplicon is a piece of DNA or RNA that is the source and/or product of amplification (molecular biology), amplification or DNA replication, replication events. It can be formed artificially, using various methods including ...

sequencing. In its heart the pipeline performs quality control over the input sequencing reads,

cluster may refer to: Science and technology Astronomy * Cluster (spacecraft), constellation of four European Space Agency spacecraft * Asteroid cluster, a small asteroid family * Cluster II (spacecraft), a European Space Agency mission to study t ...

s the marker gene nucleotide sequences at a requested

phylogenetic In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...

level (e.g. 97% for species level) into

OTUs Otus may refer to: * Otus (education), a K-12 educational technology company * HMS ''Otus'', two ships in the Royal Navy * ''Otus'' (bird), genus of owls * Otus (mythology), giant in Greek mythology, brother of Ephialtes, one of Aloadae * Otus ...

(operational taxonomic units) or sequence variants and

taxonomically In biology, taxonomy () is the scientific study of naming, defining ( circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa (singular: taxon) and these groups are given ...

annotates them by looking for similar sequences in a reference taxonomic database. The main output from the QIIME pipeline is a feature table, which describes the abundances of each OTU or sequence variant in each sample. Additional tools that are relevant to ecological aspects of the samples being investigated are also provided within the pipeline, including

rarefaction Rarefaction is the reduction of an item's density, the opposite of compression. Like compression, which can travel in waves (sound waves, for instance), rarefaction waves also exist in nature. A common rarefaction wave is the area of low relativ ...

alpha diversity In ecology, alpha diversity (α-diversity) is the mean species diversity in a site at a local scale. The term was introduced by R. H. WhittakerWhittaker, R. H. (1960) Vegetation of the Siskiyou Mountains, Oregon and California. Ecological Monograp ...

and

beta diversity Beta (, ; uppercase , lowercase , or cursive ; grc, βῆτα, bē̂ta or ell, βήτα, víta) is the second letter of the Greek alphabet. In the system of Greek numerals, it has a value of 2. In Modern Greek, it represents the voiced labiod ...

calculations, visualizations such as principle coordinates analysis (PCoA) and much more. QIIME presents a very modular approach and allows multiple methods to be applied in many stages of the analysis. For example, the stage of sequences clustering can be performed using either UCLUST, CD-HIT,

BLAST Blast or The Blast may refer to: * Explosion, a rapid increase in volume and release of energy in an extreme manner *Detonation, an exothermic front accelerating through a medium that eventually drives a shock front Film * ''Blast'' (1997 film) ...

and more. QIIME is under active development since its release in 2010.

References

External links

* {{official website, https://qiime.org Bioinformatics software Metagenomics

See also

References

External links