QC & Assembly

Flow diagram that shows the steps: Sequence reads, Quality control, Assembly, Binning and Taxonomy

A metagenome is a collection of genomic sequences from various (micro) organisms coexisting in a sample. They are snapshots that tell us about the taxonomic, metabolic or functional composition of the communities that we study.

In this lesson we will discuss how to define metagenomics and consider the challenges that this type of analysis can present. We will also discuss a workflow for metagenomics analysis.

We will then log into our cloud instance and take a look at some data. Then, we’ll go through the first two steps in our workflow: quality control and metagenome assembly.

By the end of this lesson you will be able to:

explain what metagenomics is, and the challenges it presents
interpret a FastQC plot summarizing per-base quality across all reads.
interpret the NanoPlot output summarizing a Nanopore sequencing run
filter Nanopore reads based on quality using the command line tool SeqKit
run a metagenomic assembly workflow
assess the quality of an assembly using SeqKit

IMPORTANT

You should be aware that some of the analyses in this lesson can take several hours to run - these will be completed outside of the taught lesson. You will receive guidance about this from your course instructors.