New paper in Nature Biotechnology!

We are happy to announce that Hagay Enav’s powerful new tool SynTracker is now explained in a Nature Biotechnology publication. You can access the open access paper here. A “Research Briefing” explaining how the paper was conceived is here. To use SynTracker, the code and manual are available here.

Hagay developed SynTracker, a tool to track conspecific microbial strains using genome synteny. SynTracker is sensitive to genomic structural variation but not to single-nucleotide polymorphisms (SNPs). Combining SynTracker with methods for tracking strains using SNP profiles, we were able to detect species evolving by accumulating predominantly SNPs or predominantly structural variants.

Although SynTracker can be used as a stand-alone tool, when used in combination with a SNP-based tool it can reveal how strain diversity is generated in different species.

SynTracker can be applied to various data types, ranging from data
from pure cultures of prokaryotes to that from multi-species assemblages, such as microbiomes. It also performs well for phages and plasmids. SynTracker can be used to assess strain diversity for plasmids and viruses or phages.

Now that structural variation and point mutations can be simultaneously assessed for hundreds to thousands of species, questions about the conditions that lead to strain variation being generated by predominantly one mode or the other can now be addressed.

To facilitate the use of SynTracker we are developing tools to automate downstream analyses that use the output from SynTracker. By doing so, we hope to enable users at any experience level to incorporate synteny-based analysis into their portfolios.