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Genome Assembly (SPAdes) -- GVA2021

Genome Assembly (SPAdes) -- GVA2021

Overview

SPAdes is a De Bruijn graph assembler which has become the preferred assembler in numerous labs and workflows. In this tutorial we will use SPAdes to assemble an E. coli genome from simulated Illumina reads. Genome assembly is quite difficult (though if Oxford Nanopore lowers its error rate assembly will likely get much easier and involve new tools). Genome assembly should only be used when you can not find a reference genome that is close to your own, if you are engaged in metagenomic projects where you don't know what organisms may be present, and in situations where you believe you may have novel sequence insertions into a genome of interest (Note that in this case however you would actually want to grab reads that do not map to your reference genome (and their pair in the case of paired end and mate-pair sequencing) rather than performing these functions on the fastq files you get from the raw sequencing.

A note about read preprocessing

While not explicitly covered here, the presence of adapter sequences on reads when trying to assemble them can significantly complicate assembly and harm it. If using this tutorial on your own samples make sure you are working with the best data possible .. reads lacking adapters in this case.

For those looking for a real challenge, go through the multiqc tutorial and the trimmomatic tutorial, and use the information provided here to compare assemblies of some of the same samples in both cases.


Learning Objectives

  • Run SPAdes to perform de novo assembly on fragment, paired-end, and mate-paired data.
  • Use contig_stats.pl to display assembly statistics.
  • Find proteins of interest in an assembly using Blast.


Installing SPAdes

As genome assembly is important part of analysis but is building a reference file that will be used many times, it makes more sense to install it its own environment. Other potential tools to have in the same environment would be read preprocessing tools, in particular adapter removal tools such as trimmomatic.

conda create --name GVA-SPAdes -c bioconda spades


Testing SPAdes installation

SPAdes comes with a self test option to make sure that the program