{"id":195,"date":"2017-08-26T14:03:32","date_gmt":"2017-08-26T06:03:32","guid":{"rendered":"http:\/\/www.zhanyuwang.xin\/wordpress\/?p=195"},"modified":"2017-08-26T14:03:32","modified_gmt":"2017-08-26T06:03:32","slug":"sgs-genome-assembly-platform","status":"publish","type":"post","link":"http:\/\/www.zhanyuwang.xin\/wordpress\/index.php\/2017\/08\/26\/sgs-genome-assembly-platform\/","title":{"rendered":"SGS genome assembly Platform"},"content":{"rendered":"<h2><a href=\"http:\/\/search.proquest.com\/openview\/394413fef0baa08f4b7353122cdf7b29\/1?pq-origsite=gscholar&amp;cbl=44267\">2010 Sequencing technologies \u2014 the next generation<\/a><\/h2>\n<ul>\n<li>Human Genome Sequencing\u00a0Center and Department of Molecular &amp; Human Genetics, Baylor College of Medicine<\/li>\n<li>Nature reviews<\/li>\n<\/ul>\n<p>Demand has never been greater for revolutionary technologies that deliver\u00a0fast, inexpensive and accurate genome information. This challenge has catalysed the\u00a0development of next-generation sequencing (NGS) technologies. The inexpensive\u00a0production of large volumes of sequence data is the primary advantage over conventional\u00a0methods. Here, I present a technical review of template preparation, sequencing and\u00a0imaging, genome alignment and assembly approaches, and recent advances in current\u00a0and near-term commercially available NGS instruments. I also outline the broad range of\u00a0applications for NGS technologies, in addition to providing guidelines for platform\u00a0selection to address biological questions of interest.<\/p>\n<h2><a href=\"http:\/\/downloads.hindawi.com\/journals\/biomed\/2012\/251364.pdf\">2012 Comparison of Next-Generation Sequencing Systems<\/a><\/h2>\n<ul>\n<li>NGS Sequencing Department, Beijing Genomics Institute (BGI)<\/li>\n<\/ul>\n<p>With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is\u00a0within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities.\u00a0NGS systems are typically represented by SOLiD\/Ion Torrent PGM from Life Sciences, Genome Analyzer\/HiSeq 2000\/MiSeq from\u00a0Illumina, and GS FLX Titanium\/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world\u2019s biggest\u00a0sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one\u00a0454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this\u00a0paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to\u00a0discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.<\/p>\n<h2 class=\"ArticleTitle\" lang=\"en\"><a href=\"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/1471-2164-13-341\">2012 A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers<\/a><\/h2>\n<ul class=\"u-listReset\">\n<li class=\"tooltip-tether__indexed-item\">Wellcome Trust Sanger Institute<\/li>\n<li><a class=\"journal-header__title-text\" href=\"https:\/\/bmcgenomics.biomedcentral.com\/\">BMC Genomics<\/a><\/li>\n<\/ul>\n<p>Sequence generated by Ion Torrent, MiSeq and Pacific Biosciences technologies displays near perfect coverage behaviour on GC-rich, neutral and moderately AT-rich genomes, but a profound bias was observed upon sequencing the extremely AT-rich genome of\u00a0<em class=\"EmphasisTypeItalic\">Plasmodium falciparum<\/em>\u00a0on the PGM, resulting in no coverage for approximately 30% of the genome. We analysed the ability to call variants from each platform and found that we could call slightly more variants from Ion Torrent data compared to MiSeq data, but at the expense of a higher false positive rate. Variant calling from Pacific Biosciences data was possible but higher coverage depth was required. Context specific errors were observed in both PGM and MiSeq data, but not in that from the Pacific Biosciences platform.<\/p>\n<h2><a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0168952514001127\">2014 Ten years of next-generation sequencing technology<\/a><\/h2>\n<ul>\n<li>Centre de Ge\u00b4ne\u00b4tique Mole\u00b4 culaire \u2013 CNRS<\/li>\n<li>Trends in genetics<\/li>\n<\/ul>\n<p>Ten years ago next-generation sequencing (NGS) technologies\u00a0appeared on the market. During the past decade,\u00a0tremendous progress has been made in terms of\u00a0speed, read length, and throughput, along with a sharp reduction in per-base cost. Together, these advances democratized NGS and paved the way for the development\u00a0of a large number of novel NGS applications in basic science as well as in translational research areas such as clinical diagnostics, agrigenomics, and forensic\u00a0science. Here we provide an overview of the evolution of\u00a0NGS and discuss the most significant improvements in\u00a0sequencing technologies and library preparation protocols.\u00a0We also explore the current landscape of NGS\u00a0applications and provide a perspective for future developments.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>2010 Sequencing technologies \u2014 the next generation Human Genome Sequencing\u00a0Center and Department of Molecular &amp; Human Genetics, Baylor College of Medicine Nature reviews Demand has never been greater for revolutionary technologies that deliver\u00a0fast, inexpensive and accurate genome information. This challenge has catalysed the\u00a0development of next-generation sequencing (NGS) technologies. The inexpensive\u00a0production [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[2],"tags":[],"class_list":["post-195","post","type-post","status-publish","format-standard","hentry","category-bioinformatics"],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.zhanyuwang.xin\/wordpress\/index.php\/wp-json\/wp\/v2\/posts\/195"}],"collection":[{"href":"http:\/\/www.zhanyuwang.xin\/wordpress\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.zhanyuwang.xin\/wordpress\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.zhanyuwang.xin\/wordpress\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.zhanyuwang.xin\/wordpress\/index.php\/wp-json\/wp\/v2\/comments?post=195"}],"version-history":[{"count":0,"href":"http:\/\/www.zhanyuwang.xin\/wordpress\/index.php\/wp-json\/wp\/v2\/posts\/195\/revisions"}],"wp:attachment":[{"href":"http:\/\/www.zhanyuwang.xin\/wordpress\/index.php\/wp-json\/wp\/v2\/media?parent=195"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.zhanyuwang.xin\/wordpress\/index.php\/wp-json\/wp\/v2\/categories?post=195"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.zhanyuwang.xin\/wordpress\/index.php\/wp-json\/wp\/v2\/tags?post=195"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}