{"id":13016,"date":"2018-10-15T11:35:05","date_gmt":"2018-10-15T18:35:05","guid":{"rendered":"https:\/\/www.darkenergybiosphere.org\/?post_type=publication&#038;p=13016"},"modified":"2018-11-01T13:04:10","modified_gmt":"2018-11-01T20:04:10","slug":"high-quality-genome-sequences-of-uncultured-microbes-by-assembly-of-read-clouds","status":"publish","type":"publication","link":"https:\/\/www.darkenergybiosphere.org\/publication\/high-quality-genome-sequences-of-uncultured-microbes-by-assembly-of-read-clouds\/","title":{"rendered":"High-quality genome sequences of uncultured microbes by assembly of read clouds"},"content":{"rendered":"<p>Although shotgun metagenomic sequencing of microbiome samples enables partial reconstruction of strain-level community structure, obtaining high-quality microbial genome drafts without isolation and culture remains difficult. Here, we present an application of read clouds, short-read sequences tagged with long-range information, to microbiome samples. We present Athena, a\u00a0<i>de novo<\/i>\u00a0assembler that uses read clouds to improve metagenomic assemblies. We applied this approach to sequence stool samples from two healthy individuals and compared it with existing short-read and synthetic long-read metagenomic sequencing techniques. Read-cloud metagenomic sequencing and Athena assembly produced the most comprehensive individual genome drafts with high contiguity (&gt;200-kb N50, fewer than ten contigs), even for bacteria with relatively low (20\u00d7) raw short-read-sequence coverage. We also sequenced a complex marine-sediment sample and generated 24 intermediate-quality genome drafts (&gt;70% complete, &lt;10% contaminated), nine of which were complete (&gt;90% complete, &lt;5% contaminated). Our approach allows for culture-free generation of high-quality microbial genome drafts by using a single shotgun experiment.<\/p>\n","protected":false},"template":"","tags":[],"publication_type":[19],"_links":{"self":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/publication\/13016"}],"collection":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/publication"}],"about":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/types\/publication"}],"wp:attachment":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/media?parent=13016"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/tags?post=13016"},{"taxonomy":"publication_type","embeddable":true,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/publication_type?post=13016"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}