Workshops and courses
Learning Pathway Introduction to Galaxy and Sequence analysis
Date: No date given
This learning path aims to teach you the basics of Galaxy and analysis of sequencing data.
You will learn how to use Galaxy for analysis, and will be guided through the most common
first steps of any genome analysis; quality control and a mapping or assembly of your genomic
sequences.
Keywords: beginner
Learning objectives:
- Annotate the assembly and view
- Assemble a chloroplast genome from long reads
- Assess long reads FASTQ quality using Nanoplot and PycoQC
- Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
- Explain what is a BAM file and what it contains
- Familiarize yourself with the basics of Galaxy
- Learn how histories work
- Learn how to create a workflow
- Learn how to extract and run a workflow
- Learn how to obtain data from external sources
- Learn how to run tools
- Learn how to share a history
- Learn how to share your work
- Learn how to upload a file
- Learn how to use a tool
- Learn how to view histories
- Learn how to view results
- Map reads to the assembly and view
- Perform quality correction with Cutadapt (short reads)
- Polish the assembly with short reads
- Process single-end and paired-end data
- Run a tool to map reads to a reference genome
- Summarise quality metrics MultiQC
- Use genome browser to understand your data
- assemble some paired end reads using Velvet
- examine the output of the assembly.
Event types:
- Workshops and courses
Sponsors: Australian BioCommons, ELIXIR Europe, Erasmus Medical Center, The Pennsylvania State University, University of Freiburg, de.NBI
Scientific topics: Mapping
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