Metagenomic assembly with Linked-Read Sequencing
Short-read sequencing and assembly have allowed scientists to study microbial genomes from uncultured samples, advancing the study of microbiomes beyond the minority of organisms that can be isolated and cultured. These metagenomic methods have catapulted us to a new level of understanding of the invisible microbial communities that live in, on and around us. However, the genome assemblies produced by standard short-read methods are highly fragmented and fall short of revealing the precise gene coding potential and functional capabilities of the organisms within these complex systems.
To overcome the shortcomings of short-read metagenomic shotgun sequencing, Dr. Bhatt and her lab developed Athena, a computational pipeline that uses 10x Genomics Linked-Reads to generate high-quality metagenomic assemblies from uncultured microbes (Bishara et al., 2009). To build metagenome assemblies, Athena uses Read Clouds, groups of Linked-Reads sharing the same barcode and originating from the same DNA molecule. The method was tested on microbiome samples from human stool and marine sediment. Compared with results from existing short-read and synthetic long-read metagenomic sequencing techniques, the Athena assemblies are the most contiguous reported to date.
To learn more about Athena for metagenomic de novo assembly, please join us next Wednesday for a live webinar by guest speaker, Dr. Ami Bhatt.
Date & Time: February 13, 2019 | 9AM - 10AM PT
Can’t make it? No problem, all registrants will receive an email when the webinar recording is available.
References and Additional Reading
Bishara et al., High-quality genome sequences of uncultured microbes by assembly of read clouds. Nat.... (The Athena publication)
Danko et al., Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for meta.... ( Minerva is a graph-based algorithm to deconvolute Linked-Read barcodes for metagenomic data)
Learn more about the Chromium Genome Solution and Linked-Read sequencing.