Abstract
Although shotgun metagenomic sequencing of microbiome samples enables partial reconstruction of the strain-level community structure, it remains difficult to obtain high-quality microbial genome drafts without isolation and culture. Here we present a novel application of read clouds, short read sequences tagged with long-range information, to microbiome samples. We present Athena, a de novo assembler that uses read clouds to improve metagenomic assemblies. We apply this approach to sequence stool samples from two healthy individuals, and compare it to existing short-read and synthetic long-read metagenomic sequencing techniques. Read cloud metagenomic sequencing and Athena assembly produce the most complete individual genome drafts with high contiguity (>200 kbp N50, <10 contigs), even for bacteria that have relatively low (20x) raw short-read sequence coverage. We also sequence a complex marine sediment sample and generate 24 intermediate-quality genome drafts (>70% complete, <10% contaminated), nine of which are complete (>90% complete, <5% contaminated). Thus, our approach allows culture-free generation of high-quality microbial genome drafts using a single shotgun experiment.
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.