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 New Hampshire-INBRE through an Institutional Development Award (IDeA), P20GM103506, from the National Institute of General Medical Sciences of the NIH. The work is also supported by IPERT Grant 1R25GM125674-01 from the National Institute of General Medical Sciences of the NIH.

Bioinformatic Tutorials on the Command-Line

• 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 annotatio 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

If you don’t have command-line access:

• Genetic relatedness analysis.
  • https://github.com/Joseph7e/genetic-relatedness

Additional Resources

Learning Python

https://automatetheboringstuff.com/#toc

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

Contents on this page can also be found on the centralized GitHub page https://github.com/Joseph7e/Bioinformatic-Tutorials