Introduction to Galaxy and Sequence analysis
Licence: Creative Commons Attribution 4.0 International
Keywords: introduction, Sequence Analysis, Assembly
Status: Active
Module 1: Introduction to Galaxy [and Sequence analysis]
• beginner 2 materialsGet a first look at the Galaxy platform for data analysis. We start with a short introduction (video slides & practical) to familiarize you with the Galaxy interface, and then proceed with a slightly longer introduction tutorials where you perform a first, very simple, analysis.
Time estimation: 1 hour 40 minutes
Learning objectives:
- Learn how to upload a file
- Learn how to use a tool
- Learn how to view results
- Learn how to view histories
- Learn how to extract and run a workflow
- Learn how to share a history
- Familiarize yourself with the basics of Galaxy
- Learn how to obtain data from external sources
- Learn how to run tools
- Learn how histories work
- Learn how to create a workflow
- Learn how to share your work
Module 2: Basics of Genome Sequence Analysis
• beginner 4 materialsWhen analysing sequencing data, you should always start with a quality control step to clean your data and make sure your data is good enough to answer your research question. After this step, you will often proceed with a mapping (alignment) or genome assembly step, depending on whether you have a reference genome to work with.
Time estimation: 5 hours
Learning objectives:
- Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
- Assess long reads FASTQ quality using Nanoplot and PycoQC
- Perform quality correction with Cutadapt (short reads)
- Summarise quality metrics MultiQC
- Process single-end and paired-end data
- Run a tool to map reads to a reference genome
- Explain what is a BAM file and what it contains
- Use genome browser to understand your data
- assemble some paired end reads using Velvet
- examine the output of the assembly.
- Assemble a chloroplast genome from long reads
- Polish the assembly with short reads
- Annotate the assembly and view
- Map reads to the assembly and view
Activity log