Course: Analyzing amplicon sequencing data with Qiime 2 - Pt. 1

Course: Analyzing amplicon sequencing data with Qiime 2 - Pt. 1
Christian Diener, PhD
Washington Research Foundation Distinguished Research Scientist, ISB
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[@szymonjakubowski3574]

5:11 Introduction to QUIIME 2 notebook, setting up enviorment
10:45 Introduction to QUIIME alghorytm
17:07 16SrRNA amplicon sequencing vs shotgun metagenomics
21:40 Metagenomics use in diagnosing recurrent C.differens infection
27:49 General workflow in QUIIME 16SrRNA analysis
28:44 Illumina FastQ file structure
36:03 Running first QUIMME command- importing fastq data as artifacts
41:57 Demultiplexing, creating quality visualisations of demultiplexed data
49:51 Denoising amplicon sequence variants in QUIIME
52:10 DADA2- plugin functions
54:10 DADA2- ASV Identification
57:19 DADA2- PCR Chimeras problem
1:01:42 DADA2- Merging
1:04:34 DADA2- visualisations
1:07:29 Diversity metrics- alpha and beta diversity
1:19:24 Principal Coordinate Analysis (PCoA) in phylogenetic tree construction
1:22:50 Beta diversity: 3D Emperor visualisation of PCoA
1:23:40 Statistical tests for beta diversity with PERMANOVA
1:27:57 Creating taxonomy based on sequences with Multinomial Naive Bayes
1:35:12 Final barplot visualisations
1:38:40 Creating heatmap of microbiota for samples

[@Caroline-vy1co]

Thanks for sharing this! it was very helpful.

[@asadhaq7819]

Dear Christian Diener, Thanks a lot for such an informative video presentation. It is a problem solver for me. However, I lost the track before Excercise 2. What is the code just before the Excercise 2> Secondly, can we use this program to analyze our own data?

[@ikraminf]

Thanks for sharing such an informative video.
I wanted to know what things metadata.tsv file contains i.e., the column names?

[@adeelabbasi7375]

important question. can we perform QIIME2 analysis in a 24 hour time for 16 samples of roughly 100K reads each.????

[@soulbrother12]

Question: At 49:05 you mention that cutting off the first nt´s would be conservative...what exactly do you mean by that ( gerne auch auf deutsch :-) )
And thanks so much for the upload!!!

[@AqleemAbbas]

It means the first nts have normally high quality do just remove barcode & adaper