Glossary

16s rRNA

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Alpha Diversity

Definition for this term

Barcode

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Beta Diversity

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BIOM

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FASTQ

nucleotide sequencing file that contains both information about a sequencing read (ATCG) and information about each nucleotides read quality off the sequencer (Phred score).

HPC cluster

High Performance Cluster. A network of powerful servers which can drastically increase speed and efficentcy of intestive computational processes.

MacQIIME

"MacQIIME is a precompiled installation of QIIME, with all its dependencies, placed in one easy-to-install and easy-to-update folder. It will install (and can be quickly deleted, if you like) in Mac OS 10.6 and up. It will not replace, modify or break any existing software on your computer." - Werner Lab

Metagenomics

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Microbiome

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OTU Table

A table that includes the abundances for each OTU for every sample. Typically the file is in .biom format for easier storage.

Parameters File

File used for customizing work flow scripts. http://qiime.org/documentation/qiime_parameters_files.html#format

Python

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QIIME

A comprehensive python package to help analyze, process and plot 16s rRNA microbiome

Rarefaction

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UNIX

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LEfSe

A tool developed by the Huttenhower group to find biomarker bacteria between 2 or more groups based on relative abunances.