Microbiome Bioinformatics with QIIME 2: Free online workshop

Overview

The QIIME 2 team is very excited to announce the formal launch of our official YouTube Channel! To celebrate this, we have a special gift for the QIIME 2 community - we are making our official QIIME 2 workshop content available to all, for free, to be viewed whenever and wherever!


The video playlist can be found here, bookmark this for access to the videos as they are released:

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Workshop Playlist


The content that we’ll be releasing is pre-recorded lectures and hands-on tutorials from our most recent two workshops, which were both held online. We imagine that these could be watched as they’re released (see schedule below) simulating a semester-long course; they could be watched individually if there are only specific topics that you’re interested in (though some videos refer to content or interactive steps performed in other videos); or they could be watched over the course of a few days to simulate a multi-day course, once the initial content is all available. You can also feel free to use these in workshops that you host.

Schedule

We will release one or two videos every Tuesday from now until June 2021, the videos will be published on our YouTube Channel, and will be appended to the playlist linked to above. This will give us enough time to perform light editing, and also to prepare closed-captioning for each video. The tentative schedule is listed here:

Date Topic(s)
1/26/2021 Introduction (@gregcaporaso)
2/2/2021 Semantic types and data formats (@thermokarst)
2/9/2021 Command Line Interface refresher (@gregcaporaso)
2/16/2021 PD Mice: Study background and information (@jwdebelius)
2/23/2021 Sample Metadata (@jwdebelius); PD Mice: Sample metadata (@andrewsanchez)
3/2/2021 16S Lab protocols (@emilyborsom); Using QIIME 2 View (@gregcaporaso)
3/9/2021 Importing and demultiplexing (@Mehrbod_Estaki); PD Mice: Importing demultiplexed sequences (@cherman2)
3/16/2021 Denoising (@Mehrbod_Estaki); PD Mice: Denoising (@cherman2)
3/23/2021 PD Mice: Phylogenetic reconstruction (@cherman2); Phylogenetic reconstruction (@SoilRotifer)
3/30/2021 Taxonomic assignment (@BenKaehler); PD Mice: Taxonomic classification (@Oddant1)
4/6/2021 Rarefaction (@hdeel); PD Mice: Even Sampling Depth (@thermokarst)
4/13/2021 PD Mice: Core metrics phylogenetic (@ChrisKeefe)
4/20/2021 Alpha diversity metrics (@jwdebelius); PD Mice: Alpha diversity visualizations (@ChrisKeefe)
4/27/2021 Beta diversity metrics (@aeriel.belk & @yoshiki); PD Mice: Beta diversity visualizations (@ChrisKeefe)
5/4/2021 Differential abundance testing (@mortonjt); PD Mice: ANCOM differential abundance (@ebolyen)
5/11/2021 Sample classification (@adamova); PD Mice: Sample Classification (@Oddant1)
5/18/2021 Longitudinal analyses (@emmo1 & @Zach_Burcham); PD Mice: Longitudinal Analyses (@ChrisKeefe)
5/25/2021 PD Mice: Synthesis (@cherman2)
6/1/2021 Closing Session

Required Software

Unfortunately we are not able to provide a QIIME 2 cluster for this workshop, so we strongly encourage you to install QIIME 2 locally. Check out https://docs.qiime2.org for the latest installation instructions. The video content that we have prepared will include references to the workshop clusters we have used at previous online events, and will not be strictly applicable here in this setting, but you will be able to run any commands we demonstrate in the videos on your own computer.

Getting Help

We plan to answer questions about these videos as they come up on the QIIME 2 Forum. We are in the process of setting up new forum categories to facilitate discussion of these materials. We’ll post additional details on that during the week of February 8th, when we get to the first interactive steps of the workshop.

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Thank you to everyone who taught or viewed videos in this workshop series! There are now thirty videos, which have accumulated over 3,000 views, on our Microbiome Bioinformatics with QIIME 2: Free online workshop playlist, all of which have copy-edited English captions. We’re now done with this initial offering on the QIIME 2 YouTube channel.

We now plan to transition this channel to release content on new features, interfaces, and plugins available for QIIME 2, as well as other educational content on using the system. The first of these offerings is a video by @ebolyen covering the new QIIME 2 Galaxy interface - if you haven’t yet tried this graphical interface for QIIME 2, consider watching the video and trying it out. It’s very cool!

If you’re interested in generating content to be shared on the QIIME 2 YouTube channel, for example on a new plugin that you’ve developed, please get in touch to let us know. You can post your idea to the Community Contributions category on the QIIME 2 Forum.

If you’d like to be notified as new content is developed, it’s best to subscribe to the QIIME 2 YouTube channel.

As always, thanks for your interest in QIIME 2!

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