Skip to main content
It looks like you're using Internet Explorer 11 or older. This website works best with modern browsers such as the latest versions of Chrome, Firefox, Safari, and Edge. If you continue with this browser, you may see unexpected results.

Bioinformatics Self Learning Resources

Bioinformatics tools and learning resources relevant to sequencing data and other high-throughput genomic data analysis

CLC Genomics Workbench (CLC Gx)

CLC Genomics Workbench (CLC Gx) USC-logo 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

 

2019 CLC Gx onsite training

 

Start using CLC Gx

Partek Flow

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

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

 

Tutorials

 

Webinars

 

2019 Partek onsite training

 

Start using Partek Flow

Galaxy

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

 

Public Galaxy user resources

 

Start using USC local Galaxy instances