Community Highlight: Lauren Lui
Lauren Lui (LL) is a project scientist with Adam Arkin’s lab researching subsurface microbiology using metagenomics and isolate assembly. Assembling microbial genomes can be challenging. This is especially true when retrieving sequences from metagenomics data that consist of microbial communities. One way to overcome this challenge is to create circularized genomes that provide reference genomes for future assemblies and quality control.
In her latest publication, Lauren presents a new method for circularizing genomes to improve the process of assembling complete microbial genomes from metagenomics data. This process uses iterative assembly, binning, and read mapping, including new tools available in KBase. The new Apps include Unicycler for hybrid assembly of microbial isolates and Jorg for assembly and genome circulizer.
- To see the Unicycler App in action, work through the tutorial Narrative Lauren developed.
- Test drive Jorg in Beta using this beta testing Narrative.
We asked Lauren to share her research with the KBase community – responses have been edited for clarity.
How has using KBase supported your research?
(LL) As part of the ENIGMA SFA, we are attempting to sequence as many bacterial and archaeal isolate genomes as possible using hybrid assembly. Since the Unicycler App has been implemented on KBase by Jean Marc Chandonia I can show others how to do the assemblies, even if they do not have a bioinformatics background and do not have access to servers that can do these types of assemblies. Other benefits are that the provenance of the data and assembly is recorded, I can run multiple assemblies in parallel, and the assemblies can be easily shared with others in ENIGMA. I hope that this App can help empower those that want to get high quality microbial isolate assemblies to learn more about assembly and be able to do it themselves.
Sean Jungbluth implementing Jorg into KBase will also be a big help with my metagenomics work to refine genomes assembled from environmental and enrichment metagenomics samples.
How have you benefited from working with KBase?
(LL) KBase has made it easier for me to share datasets with collaborators and connect with new potential collaborators.
What is your favorite part about using KBase?
(LL) Even though I am a bioinformatician, there are some apps that I like running in KBase for convenience. It’s great to go back to a Narrative and see how everything was done later as well.
KBase Developer Spotlight
Sean Jungbluth — Jorg
John-Marc Chandonia — Unicycler
Lauren M. Lui, Torben N. Nielsen, Adam P. Arkin. A method for achieving complete microbial genomes and improving bins from metagenomics data. PLoS Comput Biol 17(5): e1008972. DOI: 10.1371/journal.pcbi.1008972