by David Edwards

In 2013, Kat and I wrote what turned out to be a very popular Beginner’s guide for comparative bacterial genome analysis. After four years and 120,000+ downloads of the guide, we thought it might be time to update the hands-on tutorial that was included. 

As with any science, there have been advances in this time. We don’t have time to update all aspects, but felt it was important to update the recommended assembler from Velvet to SPAdes. The latter has become the ‘go-to’ assembler with our lab and many others over the last few years. Unfortunately, SPAdes does not work with Windows, but Windows users can use the original Velvet assembler if they wish to attempt their own assembly.

Also, Ryan Wick in our lab has developed a way to visualise the assembly graphs produced by SPAdes and other assemblers, in the form of a software program called Bandage. This allows us to examine and compare the properties of assembly graphs, useful if you are trying to assemble the same set of reads with different methods or parameter settings. 

The other changes in version 2 are mainly to fix broken links to the E. coli sequences that have now been archived by NCBI, kindly pointed out to us by Michael Hall and others via email.

We continue to recommend Artemis and ACT for visualising and comparing annotated bacterial genome sequences, and both tools are still actively maintained at the Sanger Institute. While BRIG is no longer actively maintained, we continue to recommend it as it appears to be stable across newer versions of Java and BLAST, and it remains incredibly useful.

Hands-on tutorial v2 (6 Mb PDF): ComparativeGenomicsTutorialV2

Original article: Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data