What is Qiime2? QIIME (Quantitative Insights Into Microbial Ecology) is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 is a major revision of the original QIIME package. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. The acronym is canonically pronounced, "chime" though some people say "kime" (and that's ok). We usually use ALL CAPS and a space between QIIME and 2 when discussing the package, and "qiime" or "qiime2" when talking about invoking specific programs. Key features include: Integrated and automatic tracking of data provenance Semantic type system Plugin system for extending microbiome analysis functionality Support for multiple types of user interfaces (e.g. API, command line, graphical)

Getting data from NCBI short read archive (SRA) In this example we are downloading is amplicon from NCBI. Go to NCBI https://www.ncbi.nlm.nih.gov/ and select SRA in the database menu. Also, you can search in the project database. You can search samples of interest by description, e.g. human microbiome, or by using an SRA sample number (usually these numbers will appear in the papers as data are usually required to be deposited in a public database before publication) example. Search in the search bar for 'salt marsh amplicon'. Select a sample of interest, e.g. 16SRNA-gene-saltmarshsediment ​​​​a. What is this sample from? ​​​​b. What sequencing technology was used? ​​​​c. When was it published?

Trimming fastq reads Trimmomatic You can use the following command to trim your reads. this will remove any potential (remember to change the names of files to those you are using!) trimmomatic This tutorial run on the dataset downloaded from NCBI SRA SRR11277344 (PE reads from Amplicon data) java -jar /trimmomatic-0.36/trimmomatic-0.36.jar PE SRR11277344_pass_1.fastq.gz SRR11277344_pass_2.fastq.gz SRR11277344_pass_paired_1.fastq.gz SRR11277344_pass_unpaired_1.fastq.gz SRR11277344_pass_paired_2.fastq.gz SRR11277344_pass_unpaired_2.fastq.gz ILLUMINACLIP:/trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36

Software We will use the software on RIT bioinformatic servers for most of our data processing and analyses. To interact with the servers you will need: A terminal to connect to the servers A program to transfer files from and to your computer What is a terminal? Find out here https://cs.colby.edu/maxwell/courses/tutorials/terminal/ What is a file transfer program? Find out here

Getting your terminal ready Navigate to the folder where you will run your analysis. Hint, you will need to use cd ls pwd Types of sequence files and how do they look in a terminal? and inside? let's use head

September 2024 In this webpage, we will just cover very simple commands. basic unix commands cheatsheet! mv, cp, ls, cd, rm... not familiar? Still not familiar?

September 2024. Goals By the end of this introduction, you should be able to: Navigate and understand the directory structure. Copy, create, and edit files and directories. Compress and uncompress files. Copy files between your computer and your home directory.