Introduction

This is a table of contents to the Hubbard Center for Genome Studies bioinformatic tutorials and resources. The development of these tutorials is supported by the Center for Integrated Biomedical and Bioengineering Research (CIBBR) and New Hampshire-INBRE through an Institutional Development Award (IDeA), P20GM113131 amd P20GM103506 respectively, from the National Institute of General Medical Sciences of the NIH.

Usage of the RON server for bioinformatic training.

The use of the server for this training is available upon request to eligible participants. If the server or these tutorials are utilized for your work, please awknowledge NH-INBRE and USNH CIBBR. To request access to the RON server, please contact me. joseph.sevigny@unh.edu

Recommended training workflow

Bioinformatic Tutorials

• Introduction to BASH and the Command-line environment.
  • https://github.com/Joseph7e/HCGS-BASH-tutorial
• Whole genome sequencing, assembly, annotation, and assessment.
  • https://github.com/Joseph7e/MDIBL-T3-WGS-Tutorial
• Comparative genomics and retrieving NCBI genomes.
  • https://github.com/Joseph7e/HCGS-Comparative-Genomics
• Metabarcoding anlsysis with QIIME2.
  • https://github.com/Joseph7e/HCGS_Metabarcoding_Tutorials
• Eukaryotic genome annotation with MAKER.
  • https://github.com/Joseph7e/MAKER-genome-annotations-tutorial
• Nanopore sequencing data analysis.
  • https://github.com/Joseph7e/Nanopore-Workflow
• RNA-Seq differential expression analysis.
  • https://github.com/LawrenceGordon/Differential-Expression-Analysis
• Genetic relatedness analysis.
  • https://github.com/Joseph7e/genetic-relatedness

Additional Resources

Hubbard Center for Genome Studies YouTube tutorials

https://www.youtube.com/@hubbardcenterforgenomestud5807

National Institute of General Medical Sciences Cloud Learning Modules

https://github.com/NIGMS/NIGMS-Sandbox/tree/main

• Fundamentals of Bioinformatics - Dartmouth College
• DNA Methylation Sequencing Analysis with WGBS - University of Hawaii at Manoa
• Transcriptome Assembly Refinement and Applications - MDI Biological Laboratory
• RNAseq Differential Expression Analysis - University of Maine
• Proteome Quantification - University of Arkansas for Medical Sciences
• ATAC-Seq and Single Cell ATAC-Seq Analysis - University of Nebraska Medical Center
• Consensus Pathway Analysis in the Cloud - University of Nevada Reno
• Integrating Multi-Omics Datasets - University of North Dakota
• Metagenomics Analysis of Biofilm-Microbiome - University of South Dakota
• Introduction to Data Science for Biology - San Francisco State University
• Analysis of Biomedical Data for Biomarker Discovery - University of Rhode Island
• Biomedical Imaging Analysis using AI/ML approaches - University of Arkansas

Other online tutorials/workflows

Single-cell RNAseq tutorial - https://github.com/hbctraining/scRNA-seq_online

Build a genome network

https://qubeshub.org/community/groups/bag/workshop/2023_sixth_national_workshop/2023_workshop_materials