{"id":3365,"date":"2016-06-19T15:10:30","date_gmt":"2016-06-19T15:10:30","guid":{"rendered":"http:\/\/41j.com\/blog\/?p=3365"},"modified":"2016-06-19T15:10:30","modified_gmt":"2016-06-19T15:10:30","slug":"a-note-on-the-ion-torrent-flow-order","status":"publish","type":"post","link":"https:\/\/41j.com\/blog\/2016\/06\/a-note-on-the-ion-torrent-flow-order\/","title":{"rendered":"A Note On The Ion Torrent Flow Order"},"content":{"rendered":"<p>The Ion torrent DNA sequencers don&#8217;t just flow in A,T,G and C bases in a 4base cycle but use a more complex 32bp flow order. I was trying to figure out exactly what was going on and found <a href=\"https:\/\/ioncommunity.thermofisher.com\/message\/3145#3145\">this comment<\/a> on the ioncommunity forum which somewhat explains what&#8217;s going on. Here&#8217;s the flow order they use (32 bases long!):<\/p>\n<p style=\"text-align: center;\">TACGTACGTCTGAGCATCGATCGATGTACAGC<\/p>\n<p>The 32 base sequence, is composed of 2 16bp sub-sequences. These subsequences have the same structure but the bases are transposed. The 16bp sequences contain one flow of every base followed by every 2bp combination [1]. In the general case a string containing every possible substring of length k exactly once is called a de Bruijn sequence [2].<\/p>\n<p>Why they do this is less clear, it might be that hitting bases in order assists with phasing or other characteristic errors. It&#8217;s also possible that there are other aspects of the base flow order that improve the sequencing process.<\/p>\n<p>[1]\u00a0The following is\u00a0a verification of the statement above:<\/p>\n<p>Original Sequence:\u00a0TACGTACGTCTGAGCATCGATCGATGTACAGC<\/p>\n<p>The following are the 16bp sequences, below these I&#8217;ve labelled each base by the position it first occurs in the sequence. These patterns are identical. The conclusion is that if you swap A with C, and swap C with G you can change the first sequence into the second:<\/p>\n<p>TACGTACGTCTGAGCA<br \/>\n1234123413142432<\/p>\n<p>TCGATCGATGTACAGC<br \/>\n1234123413142432<\/p>\n<p>Taking the 12bp sequence, you can see that it contains every 2bp combination exactly one:<\/p>\n<p>TACGTCTGAGCA<br \/>\nnew@navlaptop:~\/biotech\/dnae\/floworder$ .\/a.out | sort | uniq -c<br \/>\n1 AC<br \/>\n1 AG<br \/>\n1 CA<br \/>\n1 CG<br \/>\n1 CT<br \/>\n1 GA<br \/>\n1 GC<br \/>\n1 GT<br \/>\n1 TA<br \/>\n1 TC<br \/>\n1 TG<\/p>\n<p>[2] https:\/\/en.wikipedia.org\/wiki\/De_Bruijn_sequence<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The Ion torrent DNA sequencers don&#8217;t just flow in A,T,G and C bases in a 4base cycle but use a more complex 32bp flow order. I was trying to figure out exactly what was going on and found this comment on the ioncommunity forum which somewhat explains what&#8217;s going on. Here&#8217;s the flow order they [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"closed","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":[1],"tags":[],"class_list":["post-3365","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_shortlink":"https:\/\/wp.me\/p1RRoU-Sh","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/3365","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/comments?post=3365"}],"version-history":[{"count":1,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/3365\/revisions"}],"predecessor-version":[{"id":3366,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/3365\/revisions\/3366"}],"wp:attachment":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/media?parent=3365"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/categories?post=3365"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/tags?post=3365"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}