{"id":33595,"date":"2025-12-22T14:02:31","date_gmt":"2025-12-22T19:02:31","guid":{"rendered":"https:\/\/genomequebec.wp.vortexdev.com\/?post_type=service&#038;p=33595"},"modified":"2026-01-05T13:44:51","modified_gmt":"2026-01-05T18:44:51","slug":"small-genome-sequencing","status":"publish","type":"service","link":"https:\/\/genomequebec.wp.vortexdev.com\/en\/technological-services\/small-genome-sequencing\/","title":{"rendered":"Small Genome Sequencing"},"content":{"rendered":"\n<h2 class=\"wp-block-heading has-text-align-center\" id=\"top-of-page\"><strong>Oxford Nanopore<\/strong> <strong>Technology<\/strong><\/h2>\n\n\n\n<h3 class=\"wp-block-heading has-text-align-center has-secondary-color has-text-color has-link-color wp-elements-88d592e510ca54eee557f862b90f1bb2\"><em><strong><mark style=\"background-color:rgba(0, 0, 0, 0)\" class=\"has-inline-color has-primary-color\"><strong><em>User Guide<\/em><\/strong><\/mark><\/strong><\/em><\/h3>\n\n\n\n<p>The instructions in this guide must be followed carefully to achieve the best possible results and avoid delays in processing your request.<\/p>\n\n\n\n<p>Samples that do not comply with the recommendations may be rejected without compensation.<\/p>\n\n\n\n<div style=\"height:35px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"#Starting-Material\" data-type=\"internal\" data-id=\"#Starting-Material\">Starting Material<\/a><\/li>\n\n\n\n<li><a href=\"#Requirements-Quality-and-Quantity\" data-type=\"internal\" data-id=\"#Requirements-Quality-and-Quantity\">Requirements \u2013 Quality and Quantity<\/a>\n<ul class=\"wp-block-list\">\n<li class=\"has-black-color has-text-color has-link-color wp-elements-a2842a39f19ef22e8d274deb5fc63c95\"><a href=\"#Concentration-Verification\" data-type=\"internal\" data-id=\"#Concentration-Verification\">Concentration Verification<\/a><\/li>\n\n\n\n<li class=\"has-black-color has-text-color has-link-color wp-elements-51fa5a27f2738c13fc0481c673fa4797\"><a href=\"#Purity-Verification\" data-type=\"internal\" data-id=\"#Purity-Verification\">Purity Verification<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><a href=\"#Required-containers-and-sample-identification\">Required Containers and Sample Identification<\/a><\/li>\n\n\n\n<li><a href=\"#Service-Request-Form-and-Sample-Submission\" data-type=\"internal\" data-id=\"#Service-Request-Form-and-Sample-Submission\">Service Request Form and Sample Submission<\/a><\/li>\n\n\n\n<li><a href=\"#Sample-Shipment-Preparation\" data-type=\"internal\" data-id=\"#Sample-Shipment-Preparation\">Sample Shipment Preparation<\/a><\/li>\n\n\n\n<li><a href=\"#Transmission-of-results\" data-type=\"internal\" data-id=\"#Transmission-of-results\">Transmission of Results<\/a><\/li>\n<\/ul>\n\n\n\n<div style=\"height:35px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading has-secondary-color has-text-color has-link-color wp-elements-f1ea74b888da7196577b0d8ad8e41b53\" id=\"Starting-Material\">Starting Material<\/h4>\n\n\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><thead><tr><th><strong>Starting Material<\/strong>&nbsp;<\/th><\/tr><\/thead><tbody><tr><td>Bacterial genomic DNA.&nbsp;<\/td><\/tr><tr><td>&#8211; <strong>Recommended extraction kit<\/strong>: commercial kits from NEB, QIAGEN, or Zymo.&nbsp;<br><br><strong>&#8211; In-house protocol<\/strong>: an additional purification step with a commercial kit is required.&nbsp;<br><br>If these recommendations are not followed, the quality of the sequencing may be compromised, or even result in failure.<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<div class=\"wp-block-buttons is-horizontal is-content-justification-center is-layout-flex wp-container-core-buttons-is-layout-03627597 wp-block-buttons-is-layout-flex\">\n<div class=\"wp-block-button\"><a class=\"wp-block-button__link wp-element-button\" href=\"#top-of-page\">Return to top of page<\/a><\/div>\n<\/div>\n\n\n\n<div style=\"height:35px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading has-secondary-color has-text-color has-link-color wp-elements-595d108dd02c74b57e4cb3ea226c6dd6\" id=\"Requirements-Quality-and-Quantity\">Requirements \u2013 Quality and Quantity<\/h4>\n\n\n\n<p>The quantity and quality of samples are crucial for obtaining quality sequences.<\/p>\n\n\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><thead><tr><th><strong>Sample Type<\/strong><\/th><th><strong>Quantity<\/strong><\/th><th><strong>Concentration<\/strong><\/th><th><strong>Volume<\/strong><\/th><th><strong>Quality criteria to be met<\/strong><\/th><th><strong>Recommended verification method<\/strong><\/th><th><strong>Impact on sequencing<\/strong><\/th><\/tr><\/thead><tbody><tr><td>Bacterial genomic DNA<\/td><td>3 \u00b5g<\/td><td>~ 100 ng\/\u00b5L ideally &nbsp; <br><br>Low-concentration samples produce shorter readings and generate lower sequencing yields.<\/td><td>20 \u00b5L minimum <br><br>200 \u00b5L maximum &nbsp;<\/td><td>Double stranded, intact<\/td><td>Size and integrity verified by electrophoresis gel<\/td><td><strong>Degraded\/fragmented sample<\/strong>: <br>may lead to sequencing failure resulting in lack of consensus due to absence of full reads<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<p>Samples must be eluted in 10 mM Tris buffer, pH 8.5, or nuclease-free ultrapure water<\/p>\n\n\n\n<p>The client is responsible for providing samples of good quality and in sufficient quantity. <span style=\"text-decoration: underline;\">Sequencing failures due to non-compliance with requirements will be billed.<\/span><\/p>\n\n\n\n<div class=\"wp-block-buttons is-horizontal is-content-justification-center is-layout-flex wp-container-core-buttons-is-layout-03627597 wp-block-buttons-is-layout-flex\">\n<div class=\"wp-block-button\"><a class=\"wp-block-button__link wp-element-button\" href=\"#top-of-page\">Return to top of page<\/a><\/div>\n<\/div>\n\n\n\n<div style=\"height:35px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-default\" style=\"margin-top:24px;margin-bottom:24px\"\/>\n\n\n\n<h6 class=\"wp-block-heading has-blue-800-color has-text-color has-link-color wp-elements-080973df61c8ada12f4b2bcd58e103f6\" id=\"Concentration-Verification\">Concentration Verification<\/h6>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Recommended method<\/strong>: Qubit or equivalent fluorometric method.<\/li>\n<\/ul>\n\n\n\n<p><strong>Note: <\/strong>Spectrophotometric methods such as Nanodrop are not recommended for measuring DNA concentration because they tend to overestimate the DNA concentration, particularly for low-concentration samples or those obtained from complex extractions.<\/p>\n\n\n\n<div style=\"height:35px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-default\" style=\"margin-top:24px;margin-bottom:24px\"\/>\n\n\n\n<h6 class=\"wp-block-heading has-blue-800-color has-text-color has-link-color wp-elements-49c1949e70d9027ff1f719fca426f3aa\" id=\"Purity-Verification\">Purity Verification<\/h6>\n\n\n\n<p><strong>Recommended method<\/strong>: Nanodrop or other spectrophotometric method.<\/p>\n\n\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><thead><tr><th><strong>Ratio<\/strong><\/th><th><strong>Expected value<\/strong><\/th><th><strong>Problem if out of bounds<\/strong><\/th><th><strong>Impact on sequencing<\/strong><\/th><\/tr><\/thead><tbody><tr><td>260\/280<\/td><td>Between 1.8 and 2.0<\/td><td>Contamination by proteins or phenol. Or an unstable measurement due to an insufficient concentration.<\/td><td>Poor sequencing yield or failure<\/td><\/tr><tr><td>260\/230<\/td><td>Between 2.0 and 2.2.<\/td><td>Contamination by salts, solvents, or chemical residues. Or an unstable measurement due to an insufficient concentration.<\/td><td>Poor sequencing yield or failure<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>If using a Qiagen kit<\/strong>: perform the optional PB buffer wash step to increase purity.<\/li>\n<\/ul>\n\n\n\n<div class=\"wp-block-buttons is-horizontal is-content-justification-center is-layout-flex wp-container-core-buttons-is-layout-03627597 wp-block-buttons-is-layout-flex\">\n<div class=\"wp-block-button\"><a class=\"wp-block-button__link wp-element-button\" href=\"#top-of-page\">Return to top of page<\/a><\/div>\n<\/div>\n\n\n\n<div style=\"height:35px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading has-secondary-color has-text-color has-link-color wp-elements-dbba658f65feaf71a1d85091c8e26301\" id=\"Required-containers-and-sample-identification\">Required Containers and Sample Identification<\/h4>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>16 samples or less<\/strong>: 1.5mL tube<\/li>\n\n\n\n<li><strong>17 samples or more<\/strong>: 96-well PCR plate<\/li>\n<\/ul>\n\n\n\n<p>Tube and plate identification:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Unique, short, and legible name.<\/li>\n\n\n\n<li>Identical to the name indicated on the submission form.<\/li>\n\n\n\n<li>Plate samples &#8211; <span style=\"text-decoration: underline;\">Column arrangement required<\/span>, as indicated on the form.<\/li>\n<\/ul>\n\n\n\n<p>This is to avoid any delays in processing the request.<\/p>\n\n\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><thead><tr><th><strong>Required tubes<\/strong> &nbsp;<\/th><th><strong>96-well PCR plate recommended<\/strong> &nbsp;<\/th><th><strong>96-well PCR plate not accepted<\/strong> &nbsp;<\/th><\/tr><\/thead><tbody><tr><td><strong>&#8211; 1.5mL tubes<\/strong> &nbsp;<br><br>All types of 1.5mL tubes are accepted. &nbsp;<\/td><td>&#8211; <strong>Half-skirt PCR plate<\/strong><br><br>All types of clear half-skirt 96-well PCR plates are accepted.<br><br>Example: <em>Thermo-Fast 96 PCR detection plate with flat deck; Life Technologies, Cat# AB1400L<\/em><br><br>&#8211; <strong>Full-skirt PCR plate<\/strong><br><br>All types of clear full-skirt clear 96-well PCR plates are accepted.<br><br>Example: <em>Microseal PCR plates 96-well clear; Bio-Rad, Cat#&nbsp;MSP9601<\/em> &nbsp;<\/td><td>&#8211; 96-well cell culture plates<br><br>&#8211; Opaque 96-well PCR plates &nbsp;<\/td><\/tr><tr><td>&nbsp;<\/td><td><strong>Sealing<\/strong> <strong>&nbsp;<\/strong> <br><br><strong>Required: <\/strong>8 or 12 strip caps or heat sealing <strong>&nbsp;<\/strong> <br><br><strong>To be avoided: <\/strong>adhesive sealants (risk of leakage or contamination)<\/td><td>&nbsp;<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<div class=\"wp-block-buttons is-horizontal is-content-justification-center is-layout-flex wp-container-core-buttons-is-layout-03627597 wp-block-buttons-is-layout-flex\">\n<div class=\"wp-block-button\"><a class=\"wp-block-button__link wp-element-button\" href=\"#top-of-page\">Return to top of page<\/a><\/div>\n<\/div>\n\n\n\n<div style=\"height:35px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading has-secondary-color has-text-color has-link-color wp-elements-1afbfc3d09342a442ee7af6d6f5edfd7\" id=\"Service-Request-Form-and-Sample-Submission\">Service Request Form and Sample Submission<\/h4>\n\n\n\n<p>Click on <a href=\"https:\/\/genomequebec.wp.vortexdev.com\/en\/technological-services\/centre-dexpertise-et-de-services-2\/instructions\/service-request-and-sample-submission\/\" target=\"_blank\" data-type=\"link\" data-id=\"https:\/\/genomequebec.wp.vortexdev.com\/en\/technological-services\/centre-dexpertise-et-de-services-2\/instructions\/service-request-and-sample-submission\/\" rel=\"noreferrer noopener\">service request and sample submission<\/a> to view instructions.<\/p>\n\n\n\n<div style=\"height:35px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading has-secondary-color has-text-color has-link-color wp-elements-096fea86e9448c1a40045488fbf1d398\" id=\"Sample-Shipment-Preparation\">Sample Shipment Preparation<\/h4>\n\n\n\n<p>Click on <a href=\"https:\/\/genomequebec.wp.vortexdev.com\/en\/technological-services\/centre-dexpertise-et-de-services-2\/instructions\/sample-shipment-preparation\/\" target=\"_blank\" data-type=\"link\" data-id=\"https:\/\/genomequebec.wp.vortexdev.com\/en\/technological-services\/centre-dexpertise-et-de-services-2\/instructions\/sample-shipment-preparation\/\" rel=\"noreferrer noopener\">samples shipment preparation<\/a> to view instructions.<\/p>\n\n\n\n<div style=\"height:35px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading has-secondary-color has-text-color has-link-color wp-elements-c198d007b114cae3c4e0c5cfccb510db\" id=\"Transmission-of-results\">Transmission of Results<\/h4>\n\n\n\n<p>An automated message from Nanuq is sent to the submitter as soon as the sequences are available.<\/p>\n\n\n\n<p>Sequencing results are directly accessible via the <a href=\"https:\/\/ces.genomequebec.com\/nanuqAdministration\/j_security_check?service=https%3A%2F%2Fces.genomequebec.com%2FnanuqAdministration%2Fnanuq-administration%2FwelcomeHome.do\" target=\"_blank\" rel=\"noreferrer noopener\">Nanuq<\/a> web application.<\/p>\n\n\n\n<p>Each sequencing result folder contains:<\/p>\n\n\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><thead><tr><th><strong>Bacterial genome<\/strong><\/th><\/tr><\/thead><tbody><tr><td>&#8211; A complete report with statistics and information for each sample<br><br>&#8211; Raw FASTQ files<br><br>&#8211; An assembly (.fasta)<br><br>&#8211; An annotation file (.gff)<br><br>&#8211; An annotated assembly in GenBank format (.gbk)<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<p>These files can be downloaded locally.<\/p>\n\n\n\n<p>All samples will be retained for a maximum of 2 weeks after sequencing before being destroyed.<\/p>\n\n\n\n<div class=\"wp-block-buttons is-horizontal is-content-justification-center is-layout-flex wp-container-core-buttons-is-layout-03627597 wp-block-buttons-is-layout-flex\">\n<div class=\"wp-block-button\"><a class=\"wp-block-button__link wp-element-button\" href=\"#top-of-page\">Return to top of page<\/a><\/div>\n<\/div>\n","protected":false},"featured_media":0,"parent":0,"menu_order":0,"template":"","class_list":["post-33595","service","type-service","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/genomequebec.wp.vortexdev.com\/en\/wp-json\/wp\/v2\/service\/33595","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/genomequebec.wp.vortexdev.com\/en\/wp-json\/wp\/v2\/service"}],"about":[{"href":"https:\/\/genomequebec.wp.vortexdev.com\/en\/wp-json\/wp\/v2\/types\/service"}],"wp:attachment":[{"href":"https:\/\/genomequebec.wp.vortexdev.com\/en\/wp-json\/wp\/v2\/media?parent=33595"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}