When 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