{"id":1030,"date":"2026-04-19T15:17:27","date_gmt":"2026-04-19T15:17:27","guid":{"rendered":"https:\/\/www.embl.org\/groups\/genomics\/?page_id=1030"},"modified":"2026-06-18T10:08:43","modified_gmt":"2026-06-18T10:08:43","slug":"de-novo-sequencing-re-sequencing-of-genomic-dna","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/genomics\/de-novo-sequencing-re-sequencing-of-genomic-dna\/","title":{"rendered":"De novo sequencing &amp; re-sequencing of genomic DNA"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-1\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p>You sequence an organism\u2019s DNA and either assemble the genome from scratch or compare the reads with an existing reference genome to identify genetic differences such as single nucleotide variants, small insertions\/deletions, and larger structural changes, depending on the data and analysis. These approaches are used either when no high-quality reference genome is available or when a suitable reference exists and you want to study genetic variation across samples, individuals, or conditions.<\/p>\n\n\n<style>\n    <\/style>\n\n<section id=\"wp-block-1\">\n  <div class=\"vf-card-container vf-card-container__col-4 | vf-u-fullbleed  \n  | vf-u-background-color-ui--white \">\n        <div class=\"vf-card-container__inner\">\n            <div class=\"vf-section-header | vf-u-margin__bottom--600 | vf-u-sr-only\">\n        <h2 class=\"vf-section-header__heading\" >\n        Cards    <\/h2>\n              <\/div>\n      \n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      De novo genomic DNA sequencing    <\/h3>\n                <p class=\"vf-card__text\"><em>De novo<\/em> genomic DNA sequencing is an approach in which an organism\u2019s DNA is sequenced and the genome is assembled from scratch by overlapping reads into longer sequences, such as contigs and scaffolds. It is used when no high-quality reference genome is available or when building a new reference for a genetically distinct strain, species, or population.<\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      Genomic DNA re-sequencing    <\/h3>\n                <p class=\"vf-card__text\">Genomic DNA re-sequencing is an approach in which an organism\u2019s DNA is sequenced and the reads are compared with an existing reference genome to identify genetic differences, including single nucleotide variants, small insertions\/deletions, and, depending on the data and analysis, larger structural changes. It is used when a suitable reference genome is available and you want to study genetic variation across samples, individuals, or conditions.<\/p>\n      <\/div>\n<\/article>\n\n\n\n          <\/div>\n      <\/div>\n<\/section>\n\n<style>\n    <\/style>\n\n<section id=\"wp-block-2\">\n  <div class=\"vf-card-container vf-card-container__col-3 | vf-u-fullbleed  \n  | vf-u-background-color-ui--white \">\n        <div class=\"vf-card-container__inner\">\n            <div class=\"vf-section-header | vf-u-margin__bottom--600 | vf-u-sr-only\">\n        <h2 class=\"vf-section-header__heading\" >\n        Key References    <\/h2>\n              <\/div>\n      \n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      Key References    <\/h3>\n                <p class=\"vf-card__text\"><ul>\r\n \t<li>&#8220;<em><a class=\"vf-card_link\" href=\"https:\/\/academic.oup.com\/bib\/article\/19\/1\/23\/2339783\">The present and future of de novo whole-genome assembly<\/a>&#8220;<\/em><\/li>\r\n \t<li>&#8220;<em><a class=\"vf-card_link\" href=\"https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC4059239\/\">Sequencing, Assembling, and Correcting Draft Genomes Using Recombinant Populations<\/a><\/em>&#8220;<\/li>\r\n<\/ul><\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      Key References    <\/h3>\n                <p class=\"vf-card__text\"><ul>\r\n \t<li>&#8220;<em><a class=\"vf-card_link\" href=\"https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC4441822\/\">Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches<\/a>&#8220;<\/em><\/li>\r\n \t<li>&#8220;<a class=\"vf-card_link\" href=\"https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC7547914\/\"><em>Mapping and characterization of structural variation in 17,795 human genomes<\/em><\/a>&#8220;<\/li>\r\n<\/ul><\/p>\n      <\/div>\n<\/article>\n\n\n\n          <\/div>\n      <\/div>\n<\/section>\n\n\n<hr class=\"vf-divider\">\n\n\n\n<div class=\"vf-grid | vf-grid__col-2\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<a href=\"https:\/\/www.embl.org\/groups\/genomics\/#Applications\" target=\"_blank\">\n<button class=\"vf-button vf-button--primary\">More applications<\/button>\n<\/a>\n<!--\/vf-button-->\n\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":19,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-title-left-aligned.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-1030","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/pages\/1030","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/users\/19"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/comments?post=1030"}],"version-history":[{"count":19,"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/pages\/1030\/revisions"}],"predecessor-version":[{"id":1927,"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/pages\/1030\/revisions\/1927"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/media?parent=1030"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/embl_taxonomy?post=1030"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}