{"id":1502,"date":"2013-09-27T08:26:49","date_gmt":"2013-09-27T08:26:49","guid":{"rendered":"http:\/\/biosi.subsite.cf.ac.uk\/biosi\/kille-morgan\/hot-paper-optimization-of-de-novo-transcriptome-assembly\/"},"modified":"2015-06-19T09:51:26","modified_gmt":"2015-06-19T09:51:26","slug":"hot-paper-optimization-of-de-novo-transcriptome-assembly","status":"publish","type":"post","link":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/2013\/09\/27\/hot-paper-optimization-of-de-novo-transcriptome-assembly\/","title":{"rendered":"Hot Paper! Optimization of de novo transcriptome assembly"},"content":{"rendered":"

Optimization of de novo<\/em> transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms<\/h1>\n

Berat Z Haznedaroglu<\/strong>1<\/a>, Darryl Reeves<\/strong>2<\/a>, Hamid Rismani-Yazdi<\/strong>1<\/a>3<\/a> and Jordan Peccia<\/strong>1<\/a>*<\/p>\n

BMC Bioinformatics<\/em> 2012, 13<\/strong>:170 doi:10.1186\/1471-2105-13-170<\/p>\n

Background<\/h4>\n

The k<\/em>-mer hash length is a key factor affecting the output of de novo<\/em> transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k<\/em>-mer choices might result in the loss of unique contiguous sequences (contigs) and relevant biological information. A common solution to this problem is the clustering of single k<\/em>-mer assemblies. Even though annotation is one of the primary goals of a transcriptome assembly, the success of assembly strategies does not consider the impact of k<\/em>-mer selection on the annotation output. This study provides an in-depth k<\/em>-mer selection analysis that is focused on the degree of functional annotation achieved for a non-model organism where no reference genome information is available. Individual k<\/em>-mers and clustered assemblies (CA) were considered using three representative software packages. Pair-wise comparison analyses (between individual k<\/em>-mers and CAs) were produced to reveal missing Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog identifiers (KOIs), and to determine a strategy that maximizes the recovery of biological information in a de novo<\/em> transcriptome assembly.<\/p>\n

See suggested Work-flow in Supplementary information<\/p>\n

Professor Peter Kille,<\/p>\n

Cardiff School of Biosciences (BIOSI 1),
\nCardiff University,
\nMain Building,
\nCardiff
\nCF10 3AT<\/p>\n

Tel: +44 (0)29 20874507
\nMobile: 07870655403
\nEmail: Kille@cardiff.ac.uk<\/p>\n

http:\/\/biosi.subsite.cf.ac.uk\/biosi\/kille-morgan\/<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms Berat Z Haznedaroglu1, Darryl Reeves2, Hamid Rismani-Yazdi13 and Jordan Peccia1* BMC Bioinformatics 2012, 13:170 doi:10.1186\/1471-2105-13-170 Background The k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph<\/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-1502","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-oe","meta_box":[],"_links":{"self":[{"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/posts\/1502","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=1502"}],"version-history":[{"count":1,"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/posts\/1502\/revisions"}],"predecessor-version":[{"id":2589,"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/posts\/1502\/revisions\/2589"}],"wp:attachment":[{"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/media?parent=1502"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/categories?post=1502"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/sites.cardiff.ac.uk\/kille-morgan\/wp-json\/wp\/v2\/tags?post=1502"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}