MinION Mk1B user manual
MinION: Protocol
MinION Mk1B user manual V CTE_1000_v1_revAY_17Nov2015
Checking the MinION™ Mk1B has been assembled, installed and set up correctly.
Our device FAQs are located here.
For Research Use Only
FOR RESEARCH USE ONLY
Contents
Overview
Installation
- 2. What's in the box
- 3. Installing sequencing software
- 4. Setting up the MinION Mk1B
- 5. Setting up the MinION Mk1B for Flongle
- 6. Hardware check
Pre-sequencing checks and sequencing run
Updating the software
Troubleshooting
概览
Checking the MinION™ Mk1B has been assembled, installed and set up correctly.
Our device FAQs are located here.
For Research Use Only
1. Device information
The MinION Mk1B
The Oxford Nanopore Technologies® MinION™ is an electronic device that provides the interface between the user’s computer and the nanopore sensor array. The MinION powers to the application-specific integrated circuit (ASIC), performs temperature control and transfers data to the PC through a single USB 3.0 port. The MinION Mk1B can be used with MinION flow cells and Flongle adapter and flow cells. The MinION device can be used for DNA and RNA sequencing. The MinION is operated using the MinKNOW™ software, which controls the device, experimental scripts and also performs basecalling.
The hardware
| Component | Specification |
|---|---|
| Size and weight | H 23 mm x W 33 mm x D 105 mm, 100 g |
| Power | 5 W |
| Ports | 1 x USB Type-B |
| Environmental conditions | Designed to sequence at 18°C to 25°C |
MinION Mk1B information
FAQs
Our MinION Mk1B FAQs are located here.
2. What's in the box
What's in the box
The MinION Mk1B is shipped with:
- Configuration Test Cell (CTC)
- USB cable
- Quick Start Guide
Flongle adapters are shipped with a Flongle CTC.
The components of the MinION Mk1B are shown below.
LED lights There are four LED lights on each side of the device. The LEDs on the left side of the device display the following patterns:
- (top) red LED: ON when a flow cell has been detected
- blue LED: ON when a flow cell has not been detected
- green LED: BLINKING when the flow cell has been inserted and firmware loaded
- second blue LED: BLINKING when the flow cell has been inserted and firmware loaded
The LEDs on the right side of the device display the following patterns:
- top red LED: ON when a sequencing script is running
- second red LED: ON when a flow cell has been detected
- third red LED: BLINKING when the MinKNOW software passes instructions to the MinION
- bottom red LED: BLINKING when the MinKNOW software passes instructions to the MinION
Lid The lid can be flipped open to access the flow cell housing. Clip The clip holds the flow cell or Configuration Test Cell securely in place. Configuration Test Cell (CTC) The CTC is used during the hardware check to ensure that the communication between the device and the flow cell is working correctly. USB 3.0 port The USB 3.0 port is for connecting the MinION to the host computer for powering the device and data transfer.
3. Installing sequencing software
Downloading and installing MinKNOW
All Oxford Nanopore devices use MinKNOW™ as the primary software. The MinKNOW software carries out several core tasks: data acquisition, real-time analysis and feedback, basecalling, data streaming, controlling the device, and ensuring that the platform chemistry is performing correctly to run the samples. MinKNOW takes the raw data and converts it into reads by recognition of the distinctive change in current that occurs when a DNA strand enters and leaves the pore. MinKNOW then basecalls the reads, and writes out the data into FASTQ or BAM files.
Please follow the MinKNOW protocol for information on how to install the software on Windows, Mac OS X or Linux.
4. Setting up the MinION Mk1B
仪器
- MinION Mk1B
- Configuration test cell
Insert the CTC into the MinION Mk1B.
- Clip the CTC into place in the MinION Mk1B and connect to the host computer.
- Gently press down on the CTC; there will be a slight click as the CTC clips into place.
- Close the MinION Mk1B lid.
Close the MinION Mk1B lid and connect the MinION Mk1B device to the host computer using the included USB 3.0 cable.
步骤结束
The MinION Mk1B is ready for the hardware check to be performed.
Lights will be visible inside the MinION Mk1B device and the fan may be audible.
5. Setting up the MinION Mk1B for Flongle
仪器
- MinION Mk1B
- Flongle adapter
Place the Flongle adapter into the MinION Mk1B.
The adapter should sit evenly and flat on the MinION Mk1B. This ensures the flow cell assembly is flat during the next stage.
Close the MinION Mk1B lid and connect the MinION Mk1B device to the host computer using the included USB 3.0 cable.
步骤结束
The Flongle adapter is ready for the hardware check to be performed.
Lights will be visible inside the MinION Mk1B device and the fan may be audible.
6. Hardware check
重要
硬件检测
请务必在新设备或更新软件后使用配置测试芯片（CTC）进行硬件检测。CTC已预先插入测序设备的测序芯片卡槽内。
注意： 如您使用 Flongle 测序芯片，请定期将 空 适配器插入GridION并进行硬件检测，以确保 Flongle 适配器的正常运行。如需检查设备或测序芯片卡槽，请使用 MinION CTC，此方法同样适用于使用 Flongle 测序芯片时。
Select the sequencing device connected to the computer.
打开主页（Start），选择“Hardware Check”（硬件检测）。
Click 'Start' for the check to begin.
Ensure the position selected is ready to start, as indicated on the GUI.
Using MinION flow cells: 
Using Flongle flow cells: Note: To check the Flongle adapter, insert the EMPTY adapter. To check device or position, insert only a MinION CTC. 
随即进入“Sequencing Overview”（测序概览）页面。
测序芯片下方将有进度栏显示检测进度。
下图以Flongle配置测试芯片（CTC）为例（红框内为进度栏）。
步骤结束
硬件检测历时约1分钟。
如检测 __通过__， __指示框呈绿色__。
如检测 __未通过__，则 __指示框为橙色__。
- Flongle 通过硬件检测
- MinION 通过硬件检测
- Flongle 未通过硬件检测
如硬件未通过检测，请卸下并重新插入CTC，再次运行硬件检测。如果仍未通过检测，请通过电子邮件（support@nanoporetech.com）联系我们的客服。
7. Flow cell check
测序芯片质检
在DNA/RNA文库上样前，请务必对测序芯片的活性纳米孔数进行质检。质检需在您收到测序芯片12周之内进行。Oxford Nanopore Technologies会对活性孔数量少于以下标准的芯片进行替换** ：
| 测序芯片 | 芯片上的活性孔数确保不少于 |
|---|---|
| Flongle 测序芯片 (FLO-FLG001) | 50 |
| MinION/GridION 测序芯片 | 800 |
| PromethION 测序芯片 | 5000 |
** 请注意：自收到之日起，芯片须一直贮存于Oxford Nanopore Technologies推荐的条件下。且质检结果须在质检后的两天内递交给我们。
Navigate to the Start page and select 'Flow Cell Check' to open the flow cell check page.
When you see the MinION Flow Cell type and flow cell IDs recognised has been recognised, click 'Start' to begin.
Note: For Flongle, ensure to fill in the flow cell ID.
重要
For Flongle, flow cell ID is not automatically assigned in MinKNOW. It is imperative the flow cell ID is entered in the correct format: ABC123 i.e. ([A-Z] x 3 [0-9] x 3).
The ID is case sensitive with no spaces. The MinKNOW software will not allow you to proceed until the flow cell ID has been entered correctly.
The user will be notified in the bottom right corner of the GUI if any information entered is in the wrong format or missing.
The Flongle flow cell ID is shown in the blue box below:
You will be automatically navigated to the Sequencing Overview page.
A loading bar will be displayed under the flow cell during the check.
测序芯片健康状况指示框
测序概览（Sequencing Overview）页面会显示测序芯片的质量。质量分为三个等级：
黄色!（图中Flongle测序芯片）: 活性测序孔数量低于质保范围。将芯片从测序设备中取出后重新插入，并运行测序芯片质检。如果测序芯片活性孔数仍然低于质保范围，请您发邮件至support@nanoporetech.com。
绿色√（图中MinION 测序芯片）： 活性测序孔数量在质保范围之上。
?（图中PromethION 测序芯片）： 测序芯片在本次MinKNOW使用期间还未经过质检。
请注意： 芯片质量指示框仅在当次MinKNOW使用期间可见。一旦该次使用结束，测序芯片的状态将被清除。
8. 测序并监测实验
请参阅纳米孔社区中的MinKNOW实验指南，查看如何设置测序实验及监测实验进度。
9. MinKNOW updates for Windows and Mac OS X
MinKNOW updates
Availability of updates to the MinKNOW software are indicated via the MinKNOW host settings or as a pop-up when first opening the software. The user should follow the on-screen instructions to install the new versions.
The details of the update will be communicated in Nanopore Community announcements.
We strongly recommend users to update as soon as reasonably possible after the release has been made available.
Note: Users will not be able to update their device if connected remotely or if a run is in progress.
重要
Securing custom scripts prior to updating MinKNOW
If you have created custom scripts in MinKNOW, care should be taken to store them securely so they are not overwritten during software updates.
Please also be aware that the script structure can change between MinKNOW versions; custom scripts written for one version may not be compatible with the next.
通过桌面图标打开MinKNOW用户界面，连接测序设备后，软件的自动更新程序将自动检查更新。
当有新更新可用时，将弹出一个对话框。
选择 Get Update （获取更新）以自动更新软件。
您可以跳过更新，但是我们建议您在 有可用更新时尽快更新软件。 有些更新为仪器使用必需，因此无法跳过。
请注意： 对MinION Mk1B，单击 Get Update （获取更新）将在测序仪所连计算机上打开 软件下载 页面。用户可于该页面下载更新后的 MinION 软件。
用户可以通过“Host settings”（测序设备设置）下的“Software”（软件）板块更新仪器。
导航至“Host Settings”（测序设备设置）下的“Software”（软件）板块。点击“Get Update”（获取更新）以打开安装窗口。
当软件有可下载的新版本时，界面会出现“Update”（更新）按钮。
请注意： 对MinION Mk1B，单击 Get Update （获取更新）将在测序仪所连计算机上打开软件下载页面。用户可于该页面下载更新后的 MinION 软件。
Navigate to "MinION Software" on the Software Downloads page and download and install the executable for your device.
重要
重装MinKNOW
一些情况下，您可能需要重装软件（比如如果您目前使用的MinKNOW版本存在问题）。为此，您需要首先彻底卸载当前版本。请按照“Support ”（支持）文章中的说明进行卸载：如何彻底卸载MinKNOW。
10. Updating MinKNOW for Linux
To update MinKNOW to a new version:
sudo apt clean
sudo apt update
sudo apt install ont-standalone-minknow-release
The latest version of MinKNOW will be installed. Once these commands have completed successfully without errors, reboot the device:
sudo reboot
重要
重装MinKNOW
一些情况下，您可能需要重装软件（比如如果您目前使用的MinKNOW版本存在问题）。为此，您需要首先彻底卸载当前版本。请按照“Support ”（支持）文章中的说明进行卸载：如何彻底卸载MinKNOW。
11. Export logs
Location of log files
Log files for each sequencing experiment can be found in:
Windows C:\data\logs
Mac OS X /private/var/log/MinKNOW
Linux /var/log/minknow