{"id":1499,"date":"2013-09-24T10:49:08","date_gmt":"2013-09-24T10:49:08","guid":{"rendered":"http:\/\/biosi.subsite.cf.ac.uk\/biosi\/kille-morgan\/?p=1499"},"modified":"2015-06-19T09:51:26","modified_gmt":"2015-06-19T09:51:26","slug":"hot-paper-uparse-highly-accurate-otu-sequences-from-microbial-amplicon-reads","status":"publish","type":"post","link":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/2013\/09\/24\/hot-paper-uparse-highly-accurate-otu-sequences-from-microbial-amplicon-reads\/","title":{"rendered":"Hot Paper! UPARSE: highly accurate OTU sequences from microbial amplicon reads"},"content":{"rendered":"<p>A fantastic new paper out on the UPARSE pipeline and algorithm for cleaning and clustering OTUs in microbial diversity work, from\u00a0<a href=\"http:\/\/www.nature.com\/nmeth\/journal\/vaop\/ncurrent\/full\/nmeth.2604.html#auth-1\">Robert C Edgar<\/a>. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with \u22641% incorrect bases in artificial microbial community tests, compared with &gt;3% incorrect bases commonly reported by other methods.<\/p>\n<p>Paradigm shift?<\/p>\n<p><a href=\"http:\/\/www.nature.com\/nmeth\/journal\/vaop\/ncurrent\/full\/nmeth.2604.html\">http:\/\/www.nature.com\/nmeth\/journal\/vaop\/ncurrent\/full\/nmeth.2604.html<\/a><\/p>\n<p>&#8220;UPARSE works by quality-filtering reads, trimming them to a fixed length, optionally discarding singleton reads and then clustering the remaining reads. Clustering uses UPARSE-OTU, a novel &#8216;greedy&#8217; algorithm that performs chimera filtering and OTU clustering simultaneously\u2014unlike previously developed methods, which perform chimera filtering as a separate step, if at all.&#8221;<\/p>\n<p><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-1500\" alt=\"UPARSE\" src=\"https:\/\/i0.wp.com\/sites.cardiff.ac.uk\/kille-morgan\/files\/2013\/09\/nmeth.2604-F11.jpg?resize=946%2C858\" width=\"946\" height=\"858\" \/><\/p>\n","protected":false},"excerpt":{"rendered":"<p>A fantastic new paper out on the UPARSE pipeline and algorithm for cleaning and clustering OTUs in microbial diversity work, from\u00a0Robert C Edgar. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with \u22641% incorrect bases in artificial microbial community tests, compared with &gt;3% incorrect bases commonly reported by other methods. Paradigm shift? http:\/\/www.nature.com\/nmeth\/journal\/vaop\/ncurrent\/full\/nmeth.2604.html &#8220;UPARSE<\/p>\n","protected":false},"author":3463,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[8],"tags":[],"class_list":["post-1499","post","type-post","status-publish","format-standard","hentry","category-hot-papers"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p6t6rP-ob","meta_box":[],"_links":{"self":[{"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/posts\/1499","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/users\/3463"}],"replies":[{"embeddable":true,"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/comments?post=1499"}],"version-history":[{"count":1,"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/posts\/1499\/revisions"}],"predecessor-version":[{"id":2591,"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/posts\/1499\/revisions\/2591"}],"wp:attachment":[{"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/media?parent=1499"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/categories?post=1499"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/tags?post=1499"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}