KBase community member Lauren Lui shares her perspective on two new tools in KBase for assembling genomes from metagenomic data and improving methods through hybrid assembly and circularizing genomes.
May 10, 2021

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. 

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 JungbluthJorg

Sean Jungbluth is a scientist and developer at Lawrence Berkeley National Laboratory working with KBase to build tools and develop new features to enable environmental molecular ecology. On this specific project, he designed the KBase implementation of Jorg, a new bioinformatic tool that can be used to improve draft microbial genomes.
What was exciting or challenging about the project?
(SJ) Several key features and automated steps were required in the KBase implementation of Jorg to have it operate fluidly in the KBase ecosystem. The new features, including the ability to inspect genome assemblies using popular Circos coverage visualization plots make Jorg an exciting new addition to the KBase App catalog.

John-Marc Chandonia Unicycler

John-Marc Chandonia is a computational biologist at Lawerence Berkeley National Laboratory who has contributed to KBase since its beginning. For this particular project, he wrapped the Unicycler app in order to enable the ENIGMA team to run their preferred genome assembly pipeline in KBase.
What was exciting or challenging about the project?
(JMC) Keeping up to date on the latest SDK features.

Publication: 

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

About the Authors

Ellen Dow
Ellen Dow

Ellen G. Dow, Ph.D. is a member of the outreach, communications, and user development team. Inspired by involvement in science outreach throughout graduate school, she left the bench to gain experience in informal education and cultivate community engagement from the general public to science sectors. A molecular biologist by training, Ellen applies her research experience to support scientists and develop resources for the KBase community.