Bioinformatics Self Learning Resources

CLC Genomics Workbench (CLC Gx)  offers end-to-end data analysis solutions to a comprehensive set of NGS applications.  It also includes a large collection of molecular biology tools.  Unique NGS functionalities include:

• Whole-genome and whole-exome sequencing: variant calling, fusion gene detection
• Bisulfite-seq: alignment, differential methylation
• De Novo assembly: whole genome, microbial genome, PacBio
• Phylogenetic trees

CLC Gx online tutorials

• New user training:
  • Introduction to CLC Genomics Workbench – part 1
  • Introduction to CLC Genomics Workbench – part 2
• Tutorials
  • All CLC Gx Tutorials

2019 CLC Gx onsite training

• CLC Genomics Workbench Overview slides: GxWB-Overview.pdf
• QiaSeq NGS Library Prep Kits slides: USC QIAseq CLC Presentation 2019.pdf
• Workshop Recordings:
  • Molecular Biology Tools
  • Genome Assembly and Strain Identification
  • Qiagen’s QIAseq NGS Library Prep Kits
  • Analysis of RNA-seq/microRNAseq data (hands-on)
  • Variant Detection Workflows

Start using CLC Gx

Partek Flow   can be used to analyze a large variety of NGS data. 

• Variant calling: GATK, Samtools, FreeBayers, etc.
• CNVKit
• miRNA-seq
• Metagenomics: Kraken

Tutorials

• Partek Flow Quick-start Guide
• All Partek Flow tasks

Webinars

• Webinars: Webinar recordings for various NGS data analysis

2019 Partek onsite training

• Training recording - Overview (first half hour offers an overview of Partek Flow)

Start using Partek Flow

Galaxy is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research.  It integrates hundreds of popular statistical and bioinformatical tools for genomic sequencing data analysis.  

Accessing Public Galaxy server is hindered by the data file size limit, slow speed, as well as data security.  To help USC users to truly take advantage of this powerful platform, USC Libraries Bioinformatics Services has implemented a local instance USC Galaxy for campus-wide access, as well as a Docker Galaxy that allows users to install and use the Galaxy on their own desktop and even laptop computers.

2019 USC Libraries Bioinformatics Services Galaxy Workshop – Using the USC Galaxy Platform for Bioinformatics Analyses

• Presentation slides https://libguides.usc.edu/ld.php?content_id=48735474

Public Galaxy user resources

• Galaxy 101: Getting Started
• Galaxy Video Tutorials
• Galaxy Learning Center
• Galaxy @ Biostars-Got questions?
• Galaxy Wiki
• Galaxy Video on Youtube

Start using USC local Galaxy instances