HSLS MolBio Workshops

This workshop will introduce Microbial analysis techniques, workflows, followed by software demonstration using HSLS-Licensed CLC Genomics workbench. 

Upon completion, you will be able to:

• access the CLCbio Genomics Server hosted by Pitt CRC
• overview of Microbial Genomics modules and databases in CLC
• import and assess the quality of raw data
• review amplicon based sequencing workflow - OTU clustering and abundance, Alpha/Beta diversities
• review taxonomic analysis workflow - QC, taxonomic profiling
• review functional and drug resistance analysis workflow
• visualize the data 

Target Audience

Experimental biologists seeking to analyze Microbial Genomics data generated through experiments or retrieved from a repository such as GEO. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command line interface is required.

Powerpoints

• Microbial Genomics with CLC-Gx (ppt) - presentation slides

Lecture Videos

• Microbial Genomics Data Analysis using CLC Genomics Workbench

Data Download

• ENA Browser for PRJEB9300 Dataset -  Bacteria

Software Registration

• CLC Genomics workbench - to receive the software download link and licensing information

• CRC-CLCBio Genomics server account setup- Instructions to connect to the CLCBio Genomics Server hosted at the Center for Research Computing (CRC)

Video Tutorials

• How to import reads (FASTQ files) into CLC
• Hierarchical Clustering explained (StatQuest)
• EMBL-EBI Metagenomics Bioinformatics Training Modules

Documentations

• CLC Genomics workbench v23.0.3 Manual 
• CLC Genomics Microbial Genomics Module User manual
• Statistics for Biologists -a collection highlights important statistical issues that biologists should be aware of and provides practical advice to help them improve the rigor of their work.
• FastQC Problems and Discussion 
• Data transfer using Ondemand tool in CRC

• NIH Human Microbiome Project
• MGnify - A database for Microbiome by EBI
• ENA (Europian Nucleotide Archive)
• Microbiome DB
• FASTQC - a quality control tool for high throughput sequence data
• Venn Diagram Creator 
• BioRender - Scientific illustrations creating tool

Featured Article

• Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition

Key References

• What is new and relevant for sequencing-based microbiome research? A mini-review
• A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

• A practical guide to amplicon and metagenomic analysis of microbiome data

• A Bioinformatician's Guide to Metagenomics

• MGnify: the microbiome analysis resource in 2020

Publications citing CLC-Genomics Workbench from Pitt researchers (295 as of January 17, 2023)

Attribution

Please include the following statement in the acknowledgments section for all publications, posters, and presentations: 

CLC Genomics Workbench software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh  (RRID:SCR_011975) was used for data analysis.

If you used the Pitt-CRC server for CLC Genomics Workbench, then please also include the following text in the acknowledgments section for all publications, posters, and presentations: 

This research was supported in part by the University of Pittsburgh Center for Research Computing through the resources provided.

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