文档介绍：QI I ME (pronounced "chime") stands for Quantitative I ns i ghts Into M i crob i a I EcoIogy. QIIME i s an open source software package for compar i son and ana lysis of microbiaI communities, pr imar i ly based on h i gh-throughput amp I i con sequenc i ng data
(such as SSU rRNA小亚基核糖体rna
generated on a var i ety of pIatforms, but a I so support i ng ana lysis of other types of data
(such as shotgun metagenomic data metagenomic意思是宏恳因纽学，是对环境样品中微生物群体基因组进行的分析).
QI IME takes users from the i r raw sequencing output through initial ana Iyses such as OTU p ick i ng 系统聚类，taxonomic ass ig nment 分类，and construct i on of phylogenetic trees 系统树 from representat i ve sequences of OTUs, and through downstream stat i st i cal ana lys i s, vi sua I i zat i on, and product ion of pub I icat i on-qua I i ty graphics - QI IME has been app I ied to 适用于 si n gle stud i es based on bill i ons of sequences from thousands of samp Ies •
Th i s tutor i a I exp I a i ns how to use the
QIIME (Quant itat i ve I ns i ghts Into MicrobiaI EcoIogy)
Pi pe I i ne to process data from high-throughpu t 16S rRNA seque ncing stu d i es - If you have not a I ready instaI led qi ime, pI ease see the sect i on I nsta i I i ng Qi ime f i rst - The purpose of th i s p i pe I i ne 流水线 i s to prov i de a start——to-f inish workflow, beginning with
multiplexed sequence复合序列（多序列比对，整理分类和系统文件，比较样本，确定改变微生物群体形态的生物和环境因素）
reads and finishing with taxonomic and phylogenetic prof i les and compar i sons of the samp les i n the study. With thi s i nforma t i on i n hand, it i s poss i bIe to det erm i ne biological and env i ronme ntaI fac tors that a Iter microbial comm unity ecology i n your exper iment •
As an examp Iet v/e will use data from a study of the response of mouse gut microbiaI comm unities to fas ting (Crawford et al-, 2009) - To make t h i s tu tor i a I run quickly on a perso na I compu ter, we wi I I use a subse t of the data genera ted from 5 animals kep t on the cont rol ad I ibi turn fed di