Ligation sequencing DNA XL V14 (SQK-LSK114-XL)

Version for device: MinION

1. Introduction to the Ligation Sequencing Kit XL V14 (SQK-LSK114-XL) protocol

   This protocol describes how to carry out sequencing of multiple DNA samples simultaneously using the Ligation Sequencing Kit XL V14 (SQK-LSK114-XL). It is recommended that a Lambda control experiment is completed first to become familiar with the technology.

   Steps in the sequencing workflow:

   Prepare for your experiment

   You will need to:

   • Extract your DNA, and check its length, quantity and purity. The quality checks performed during the protocol are essential in ensuring experimental success.
   • Ensure you have your sequencing kit, the correct equipment and third-party reagents
   • Download the software for acquiring and analysing your data
   • Check your flow cell to ensure it has enough pores for a good sequencing run

   
   

   Library preparation

   The table below is an overview of the steps required in the library preparation, including timings and optional stopping points.

   Library preparation	Process	Time	Stop option
   DNA repair and end-prep	Repair the DNA and prepare the DNA ends for adapter attachment	35 minutes	4°C overnight
   Adapter ligation and clean-up	Attach the sequencing adapters to the DNA ends	20 minutes	4°C short-term storage or for repeated use, such as re-loading your flow cell -80°C for single-use, long-term storage. We strongly recommend sequencing your library as soon as it is adapted.
   Priming and loading the flow cell	Prime the flow cell and load the prepared library for sequencing	5 minutes

   

   Sequencing and analysis

   You will need to:

   • Start a sequencing run using the MinKNOW software which will collect raw data from the device and basecall reads.
   • Start the EPI2ME software and select a bioinformatics workflow to analyse your data.
2. Important Compatibility of this protocol

   This protocol should only be used in combination with:

   • Ligation Sequencing Kit XL V14 (SQK-LSK114-XL)
   • Control Expansion (EXP-CTL001)
   • R10.4.1 MinION Flow Cells (FLO-MIN114)
   • Flow Cell Wash Kit (EXP-WSH004)
   • MinION Mk1B - MinION Mk1B IT requirements document
   • MinION Mk1C - MinION Mk1C IT requirements document
   • MinION Mk1D - MinION Mk1D IT requirements document
   • GridION - GridION IT requirements document

1. Adjust your sample input quantity depending on your initial DNA sample length:

   Fragment library length	Starting input
   Very short (<1 kb)	200 fmol
   Short (1-10 kb)	100–200 fmol
   Long (>10 kb)	1 µg

   For more information on sample input and flow cell loading amounts for our ligation sequencing protocols please visit our know-how document.

2. Input DNA

   How to QC your input DNA

   It is important that the input DNA meets the quantity and quality requirements. Using too little or too much DNA, or DNA of poor quality (e.g. highly fragmented or containing RNA or chemical contaminants) can affect your library preparation.

   For instructions on how to perform quality control of your DNA sample, please read the Input DNA/RNA QC protocol.

   Chemical contaminants

   Depending on how the DNA is extracted from the raw sample, certain chemical contaminants may remain in the purified DNA, which can affect library preparation efficiency and sequencing quality. Read more about contaminants on the Contaminants page of the Community.

3. NEBNext® Companion Module v2 for Oxford Nanopore Technologies® Ligation Sequencing

   We recommend buying the NEBNext® Companion Module v2 for Oxford Nanopore Technologies® Ligation Sequencing (catalogue number E7672S or E7672L), which contains all the NEB reagents needed for use with the Ligation Sequencing Kit.

   The previous version, NEBNext® Companion Module for Oxford Nanopore Technologies® Ligation Sequencing (NEB, E7180S or E7180L) is compatible, but the recommended v2 module offers more efficient dA-tailing and ligation, a result of the FFPEv2 DNA Repair Buffer and Salt-T4 DNA Ligase, respectively. A marked cost saving per sample preparation is also realised when using the v2 module.

   Note: for our amplicon protocols, NEBNext FFPE DNA Repair Mix is not required and purchasing the required reagents separately is more cost effective.

4. Multichannel pipettes

   For scaling up library prep using the Ligation Sequencing Kit XL, customers will need multichannel pipettes and appropriate pipette tips. Although the choice of brand is left to the user's discretion, our R&D team can recommend Rainin Pipet-Lite LTS L200-XLS+ (20–200 μl) and Pipet-Lit LTS L20-XLS+ (2–20 μl) pipettes and Rainin LTS pipette tips.

5. Third-party reagents

   We have validated and recommend the use of all the third-party reagents used in this protocol. Alternatives have not been tested by Oxford Nanopore Technologies.

   For all third-party reagents, we recommend following the manufacturer's instructions to prepare the reagents for use.

6. Check your flow cell

   We highly recommend that you check the number of pores in your flow cell prior to starting a sequencing experiment. This should be done within 12 weeks of purchasing for MinION/GridION/PromethION or within four weeks of purchasing Flongle Flow Cells. Oxford Nanopore Technologies will replace any flow cell with fewer than the number of pores in the table below, when the result is reported within two days of performing the flow cell check, and when the storage recommendations have been followed. To do the flow cell check, please follow the instructions in the Flow Cell Check document.

   Flow cell	Minimum number of active pores covered by warranty
   Flongle Flow Cell	50
   MinION/GridION Flow Cell	800
   PromethION Flow Cell	5000

7. Important We strongly recommend using the Ligation Buffer (LNB) supplied in the Ligation Sequencing Kit V14 rather than any third-party ligase buffers to ensure high ligation efficiency of the Ligation Adapter (LA).
8. Important Ligation Adapter (LA) included in this kit and protocol is not interchangeable with other sequencing adapters.
9. Ligation Sequencing Kit XL V14 (SQK-LSK114-XL) contents

   

   Name	Acronym	Vial colour	Number of vials	Fill volume per vial (µl)
   DNA Control Strand	DCS	Yellow	1	100
   Ligation Adapter	LA	Green	1	320
   Ligation Buffer	LNB	White	1	1,500
   Elution Buffer	EB	White cap, black strip label	1	10,000
   Long Fragment Buffer	LFB	White cap, orange strip label	2	20,000
   Short Fragment Buffer	SFB	White cap, blue strip label	2	20,000
   Library Beads	LIB	Pink	2	1,800
   Library Solution	LIS	White cap, pink label	2	1,800
   Sequencing Buffer	SB	Red	3	1,700
   Flow Cell Flush	FCF	Clear	4	15,500
   Flow Cell Tether	FCT	Purple	1	1,600

   Note: The DNA Control Sample (DCS) is a 3.6 kb standard amplicon mapping the 3' end of the Lambda genome.

1. Tip We recommend using the NEBNext® Companion Module v2 for Oxford Nanopore Technologies® Ligation Sequencing (catalogue number E7672S or E7672L), which contains all the NEB reagents needed for use with the Ligation Sequencing Kit.

   The previous version, NEBNext® Companion Module for Oxford Nanopore Technologies® Ligation Sequencing (NEB, E7180S or E7180L) is also compatible, but the recommended v2 module offers more efficient dA-tailing and ligation.

2. Check your flow cell.

   We recommend performing a flow cell check before starting your library prep to ensure you have a flow cell with enough pores for a good sequencing run.

   See the flow cell check instructions in the MinKNOW protocol for more information.

3. Important Optional fragmentation and size selection

   By default, the protocol contains no DNA fragmentation step, however in some cases it may be advantageous to fragment your sample. For example, when working with lower amounts of input gDNA (100 ng – 500 ng), fragmentation will increase the number of DNA molecules and therefore increase throughput. Instructions are available in the DNA Fragmentation section of Extraction methods.

   Additionally, we offer several options for size-selecting your DNA sample to enrich for long fragments - instructions are available in the Size Selection section of Extraction methods.

4. Thaw DNA Control Sample (DCS) at room temperature, spin down, mix by pipetting, and place on ice.
5. Prepare the NEB reagents in accordance with manufacturer’s instructions, and place on ice.

   For optimal performance, NEB recommend the following:

   1. Thaw all reagents on ice.

   2. Flick and/or invert the reagent tubes to ensure they are well mixed.
      
      Note: Do not vortex the FFPE DNA Repair Mix or Ultra II End Prep Enzyme Mix.

   3. Always spin down tubes before opening for the first time each day.

   4. Vortex the FFPE DNA Repair Buffer v2, or the NEBNext FFPE DNA Repair Buffer and Ultra II End Prep Reaction Buffer to ensure they are well mixed.
      Note: These buffers may contain a white precipitate. If this occurs, allow the mixture(s) to come to room temperature and pipette the buffer several times to break up the precipitate, followed by a quick vortex to mix.

   5. The FFPE DNA Repair Buffer may have a yellow tinge and is fine to use if yellow.

6. Prepare the DNA in nuclease-free water:
   • Transfer 1 μg (or 100-200 fmol) input DNA into a separate well of a 96-well plate or a 0.2 ml PCR tube strip
   • Adjust the volume to 47 μl with nuclease-free water
   • Mix thoroughly by pipetting up and down, or by flicking the tube
   • If necessary, seal and spin down briefly in an appropriate microfuge

7. To each sample, add the following:

   Between each addition, pipette mix 10-20 times.

   Reagent	Volume
   DNA from the previous step	47 µl
   DNA CS (optional)	1 µl
   NEBNext FFPE DNA Repair Buffer v2	7 µl
   NEBNext FFPE DNA Repair Mix	2 µl
   Ultra II End-prep Enzyme Mix	3 µl
   Total	60 µl

   
   

   If using the previous version of the NEBNext® Companion Module for Oxford Nanopore Technologies® Ligation Sequencing (NEB, E7180S or E7180L):

   Between each addition, pipette mix 10-20 times.

   Reagent	Volume
   DNA from the previous step	47 µl
   DNA CS (optional)	1 µl
   NEBNext FFPE DNA Repair Buffer	3.5 µl
   NEBNext FFPE DNA Repair Mix	2 µl
   Ultra II End-prep Reaction Buffer	3.5 µl
   Ultra II End-prep Enzyme Mix	3 µl
   Total	60 µl

8. Tip For ease, make a master mix of these reagents prior to adding to the DNA samples:
   • Combine the repair and end-prep reagents in the correct ratio and mix well by gently pipetting the entire volume up and down 10 times (ensure the total volume is enough to accommodate 13 µl being added to each DNA sample, with an excess to allow for pipetting losses).
   • Add 13 µl of the master mix to each DNA sample. This can be done by pre-aliquoting the master mix and transferring 13 µl into each sample tube simultaneously, using a multichannel pipette.
9. Mix well by gently pipetting the entire volume within each well/tube up and down 10 times, or by flicking the tubes, and spin down.
10. Seal the plate, or close the tube lids.
11. Using a thermal cycler, incubate at 20°C for 5 minutes and 65°C for 5 minutes.
12. Important AMPure XP bead clean-up

    It is recommended that the repaired/end-prepped DNA sample is subjected to the following clean-up with AMPure XP beads. This clean-up can be omitted for simplicity and to reduce library preparation time. However, it has been observed that omission of this clean-up can: reduce subsequent adapter ligation efficiency, increase the prevalence of chimeric reads, and lead to an increase in pores being unavailable for sequencing. If omitting the clean-up step, proceed to the next section.

13. Resuspend the AMPure XP beads by vortexing and transfer to a pipetting trough. Ensure that the volume transferred is enough for 60 µl to be added to each DNA sample, with an excess to allow for dead volume within the pipetting trough.
14. Important Resuspend and transfer the beads to the pipetting trough immediately before use to ensure beads do not settle.
15. Keep the DNA samples in their original wells/PCR tubes. Add 60 µl of resuspended AMPure XP beads to each sample and mix by pipetting at least 100 µl up and down ten times. Retain any unused beads.
16. Incubate for 5 minutes at room temperature.
17. Prepare fresh 80% ethanol in nuclease-free water and pour into a pipetting trough. Allow enough for 500 µl per sample, with an excess to allow for dead volume within the pipetting trough. After the bead washing steps, discard any unused ethanol.
18. Pellet the beads on a magnet for at least 2 minutes, or until the supernatant is clear. Keep the plate/tube strip on the magnet and pipette off the supernatant.
19. Keeping the plate/tube strip on the magnet, wash each pellet of beads with 200 µl of the freshly-prepared 80% ethanol without disturbing the pellets. Remove the 80% ethanol using a pipette and discard.
20. Repeat the previous step.
21. Seal the plate, or close the tube lids. Spin down and place the plate/tube strip back on the magnet. Pipette off any residual ethanol.
22. Pour nuclease-free water into a pipetting trough. Allow enough for 61 µl per sample, with an excess to allow for dead volume within the pipetting trough.
23. Remove the plate/tube strip from the magnetic rack and resuspend each pellet in 61 µl nuclease-free water from the pipetting trough. Pipette the entire volume up and down ten times).
24. Seal the plate or close the tube lids, and incubate for 2 minutes at room temperature.
25. Pellet the beads on a magnet until the eluate is clear and colourless, for at least 1 minute.
26. Remove and retain 61 µl of each eluate in a separate, clean well/tube within a 96-well PCR plate or PCR tube strip. Dispose of the pelleted beads.
27. Quantify 1 µl of eluted sample using a Qubit fluorometer.
28. End of Step Take forward the repaired and end-prepped DNA into the adapter ligation step. However, at this point it is also possible to store the sample at 4°C overnight.

1. Tip We recommend using the Salt-T4® DNA Ligase (NEB, M0467).

   Salt-T4® DNA Ligase (NEB, M0467) can be bought separately or is provided in the NEBNext® Companion Module v2 for Oxford Nanopore Technologies® Ligation Sequencing (catalogue number E7672S or E7672L).

   The Quick T4 DNA Ligase (NEB, E6057) available in the previous version NEBNext® Companion Module for Oxford Nanopore Technologies® Ligation Sequencing (NEB, E7180S or E7180L) is also compatible, but the new recommended reagent offers more efficient and ligation.

2. Important Although third-party ligase products may be supplied with their own buffer, the ligation efficiency of the Ligation Adapter (LA) is higher when using the Ligation Buffer (LNB) supplied in the Ligation Sequencing Kit.
3. Spin down the Ligation Adapter (LA) and Salt-T4® DNA Ligase, and place on ice.
4. Thaw Ligation Buffer (LNB) at room temperature, spin down and mix by pipetting. Due to viscosity, vortexing this buffer is ineffective. Place on ice immediately after thawing and mixing.
5. Thaw the Elution Buffer (EB) at room temperature and mix by vortexing. Then spin down and place on ice.
6. Important Depending on the wash buffer (LFB or SFB) used, the clean-up step after adapter ligation is designed to either enrich for DNA fragments of >3 kb, or purify all fragments equally.
   • To enrich for DNA fragments of 3 kb or longer, use Long Fragment Buffer (LFB)
   • To retain DNA fragments of all sizes, use Short Fragment Buffer (SFB)
7. Thaw either Long Fragment Buffer (LFB) or Short Fragment Buffer (SFB) at room temperature and mix by vortexing. Then spin down and place on ice.
8. Tip Once Short Fragment Buffer (SFB), Long Fragment Buffer (LFB) and Elution Buffer (EB) are thawed, they can be aliquoted and stored for up to one month at 4°C.
9. For each sample, combine the following reagents:

   Between each addition, pipette mix 10-20 times.

   Reagent	Volume
   DNA sample from the previous step	60 µl
   Ligation Adapter (LA)	5 µl
   Ligation Buffer (LNB)	25 µl
   Salt-T4® DNA Ligase	10 µl
   Total	100 µl

10. Tip For ease, you can pre-aliquot the reagents separately into empty PCR tubes, from which the reagents are transferred to the DNA samples using a multichannel pipette.

    Ensure excess volumes of the reagents are present in these tubes. Leftover reagent should be recovered. For example, for twelve separate DNA samples, aliquot:

    Reagent	Volume
    Ligation Buffer (LNB)	30 µl into each of 12 clean PCR tubes
    Salt-T4® DNA Ligase	12 µl into each of 12 clean PCR tubes
    Ligation Adapter (LA)	6 µl into each of 12 clean PCR tubes

    Alternatively, you can make a master mix of these reagents (allowing up to a 20% excess of each reagent), and add 40 μl of this to each DNA sample. However, ligation efficiency may be compromised if the master mix is not used within 10 minutes.

11. Mix well by gently pipetting the entire volume within each well/tube up and down 10 times.
12. Incubate the reaction for 10 minutes at room temperature.
13. Resuspend the AMPure XP beads by vortexing and transfer to a pipetting trough. Ensure that the volume transferred is enough for 60 µl to be added to each DNA sample, with an excess to allow for dead volume within the pipetting trough.
14. Important Resuspend and transfer the beads to the pipetting trough immediately before use to ensure beads do not settle.
15. Add 40 µl of resuspended AMPure XP beads to each sample and mix by pipetting the entire combined volume up and down 10 times.
16. Incubate for 5 minutes at room temperature.
17. Add sufficient Long Fragment Buffer (LFB) or Short Fragment Buffer (SFB) to a pipetting trough. Allow enough for 400 µl per sample, with an excess to allow for dead volume within the pipetting trough. Retain any unused reagent after the wash steps.
18. Pellet the beads on a magnet for at least 2 minutes, or until the supernatant is clear. Keep the plate/tube strip on the magnet and pipette off the supernatant.
19. Remove the plate/tube strip from the magnetic rack and wash each pellet of beads by adding either 200 μl Long Fragment Buffer (LFB) or Short Fragment Buffer (SFB). Resuspend each pellet thoroughly by pipetting the entire volume of buffer up and down ten times. Fully resuspending the beads at this step ensures optimal kit performance. Return the plate/tube strip to the magnetic rack and allow the beads to pellet until the supernatant is clear. Remove the supernatant using a pipette and discard.
20. Important It is essential that beads are resuspended fully and not simply moved around the tubes through use of the magnet.
21. Repeat the previous step.
22. Seal the plate, or close the tube lids. Spin down and place the plate/tube strip back on the magnet. Pipette off any residual supernatant.
23. Add sufficient Elution Buffer (EB) to a pipetting trough. Allow enough for 15 µl per sample, with an excess to allow for dead volume within the pipetting trough. Retain any unused Elution Buffer (EB) after the elution step.
24. Remove the plate/tube strip from the magnetic rack and resuspend each pellet in 15 µl Elution Buffer (EB) from the pipetting trough, pipetting the entire volume up and down 10 times.
25. Tip Ensure the beads are fully resuspended. Brief centrifugation can be used to help to draw liquid droplets and beads to the bottom of the wells/tubes during and after resuspension.
26. Seal the plate (or close the tube lids), and incubate for 10 minutes at 37°C in a thermal cycler. Any heated lid used should be limited to 50°C.
27. Pellet the beads on a magnet until the eluate is clear and colourless, for at least 1 minute.
28. Remove and retain 15 µl of each eluate in a separate, clean well/tube within a 96-well PCR plate or PCR tube strip. Dispose of the pelleted beads.
29. Quantify 1 µl of eluted sample using a Qubit fluorometer.
30. Depending on your DNA library fragment size, prepare your final library in 12 µl of Elution Buffer (EB).

    Fragment library length	Flow cell loading amount
    Very short (<1 kb)	100 fmol
    Short (1-10 kb)	35–50 fmol
    Long (>10 kb)	300 ng

    Note: If the library yields are below the input recommendations, load the entire library.

    If required, we recommend using a mass to mol calculator such as the NEB calculator.

31. End of Step The prepared library is used for loading into the flow cell. Store the library on ice or at 4°C until ready to load.
32. Tip Library storage recommendations

    We recommend storing libraries in Eppendorf DNA LoBind tubes at 4°C for short-term storage or repeated use, for example, re-loading flow cells between washes.
    For single use and long-term storage of more than 3 months, we recommend storing libraries at -80°C in Eppendorf DNA LoBind tubes.

1. Important Please note, this kit is only compatible with R10.4.1 flow cells (FLO-MIN114).
2. Tip Priming and loading a flow cell

   We recommend all new users watch the 'Priming and loading your flow cell' video before your first run.

3. Thaw the Sequencing Buffer (SB), Library Beads (LIB) or Library Solution (LIS, if using), Flow Cell Tether (FCT) and Flow Cell Flush (FCF) at room temperature before mixing by vortexing. Then spin down and store on ice.
4. Important For optimal sequencing performance and improved output on MinION R10.4.1 flow cells (FLO-MIN114), we recommend adding Bovine Serum Albumin (BSA) to the flow cell priming mix at a final concentration of 0.2 mg/ml.

   Note: We do not recommend using any other albumin type (e.g. recombinant human serum albumin).

5. To prepare the flow cell priming mix with BSA, combine Flow Cell Flush (FCF) and Flow Cell Tether (FCT), as directed below. Mix by pipetting at room temperature.

   Note: We are in the process of reformatting our kits with single-use tubes into a bottle format. Please follow the instructions for your kit format.

   Single-use tubes format:
   Add 5 µl Bovine Serum Albumin (BSA) at 50 mg/ml and 30 µl Flow Cell Tether (FCT) directly to a tube of Flow Cell Flush (FCF).

   Bottle format:
   In a suitable tube for the number of flow cells, combine the following reagents:

   Reagent	Volume per flow cell
   Flow Cell Flush (FCF)	1,170 µl
   Bovine Serum Albumin (BSA) at 50 mg/ml	5 µl
   Flow Cell Tether (FCT)	30 µl
   Total volume	1,205 µl

6. Open the MinION or GridION device lid and slide the flow cell under the clip. Press down firmly on the priming port cover to ensure correct thermal and electrical contact.

   

   

7. Optional Action

   Complete a flow cell check to assess the number of pores available before loading the library.

   This step can be omitted if the flow cell has been checked previously.

   See the flow cell check instructions in the MinKNOW protocol for more information.

8. Slide the flow cell priming port cover clockwise to open the priming port.

   

9. Important Take care when drawing back buffer from the flow cell. Do not remove more than 20-30 µl, and make sure that the array of pores are covered by buffer at all times. Introducing air bubbles into the array can irreversibly damage pores.
10. After opening the priming port, check for a small air bubble under the cover. Draw back a small volume to remove any bubbles:
    1. Set a P1000 pipette to 200 µl
    2. Insert the tip into the priming port
    3. Turn the wheel until the dial shows 220-230 µl, to draw back 20-30 µl, or until you can see a small volume of buffer entering the pipette tip
       

    Note: Visually check that there is continuous buffer from the priming port across the sensor array.

    

11. Load 800 µl of the priming mix into the flow cell via the priming port, avoiding the introduction of air bubbles. Wait for five minutes. During this time, prepare the library for loading by following the steps below.

    

12. Thoroughly mix the contents of the Library Beads (LIB) by pipetting.
13. Important The Library Beads (LIB) tube contains a suspension of beads. These beads settle very quickly. It is vital that they are mixed immediately before use.

    We recommend using the Library Beads (LIB) for most sequencing experiments. However, the Library Solution (LIS) is available for more viscous libraries.

14. In a new 1.5 ml Eppendorf DNA LoBind tube, prepare the library for loading as follows:

    Reagent	Volume per flow cell
    Sequencing Buffer (SB)	37.5 µl
    Library Beads (LIB) mixed immediately before use, or Library Solution (LIS), if using	25.5 µl
    DNA library	12 µl
    Total	75 µl

15. Complete the flow cell priming:
    1. Gently lift the SpotON sample port cover to make the SpotON sample port accessible.
    2. Load 200 µl of the priming mix into the flow cell priming port (not the SpotON sample port), avoiding the introduction of air bubbles.

    

    

16. Mix the prepared library gently by pipetting up and down just prior to loading.
17. Add 75 μl of the prepared library to the flow cell via the SpotON sample port in a dropwise fashion. Ensure each drop flows into the port before adding the next.

    

18. Gently replace the SpotON sample port cover, making sure the bung enters the SpotON port and close the priming port.

    

    

19. Important Install the light shield on your flow cell as soon as library has been loaded for optimal sequencing output.

    We recommend leaving the light shield on the flow cell when library is loaded, including during any washing and reloading steps. The shield can be removed when the library has been removed from the flow cell.

20. Place the light shield onto the flow cell, as follows:

    1. Carefully place the leading edge of the light shield against the clip.
       Note: Do not force the light shield underneath the clip.

    2. Gently lower the light shield onto the flow cell. The light shield should sit around the SpotON cover, covering the entire top section of the flow cell.

    

21. Caution The MinION Flow Cell Light Shield is not secured to the flow cell and careful handling is required after installation.
22. End of Step Close the device lid and set up a sequencing run on MinKNOW.

1. How to start sequencing

   Once you have loaded your flow cell, the sequencing run can be started on MinKNOW, our sequencing software that controls the device, data acquisition and real-time basecalling. For more detailed information on setting up and using MinKNOW, please see the MinKNOW protocol.

   MinKNOW can be used and set up to sequence in multiple ways:

   • On a computer either directly or remotely connected to a sequencing device.
   • Directly on a GridION or PromethION 24/48 sequencing device.

   For more information on using MinKNOW on a sequencing device, please see the device user manuals:

   • MinION Mk1B user manual
   • MinION Mk1C user manual
   • MinION Mk1D user manual
   • GridION user manual

   ---

   To start a sequencing run on MinKNOW:

   1. Navigate to the start page and click Start sequencing.

   2. Fill in your experiment details, such as name and flow cell position and sample ID.

   3. Select the sequencing kit used in the library preparation on the Kit page.

   4. Configure the sequencing and output parameters for your sequencing run or keep to the default settings on the Run configuration tab.

   Note: If basecalling was turned off when a sequencing run was set up, basecalling can be performed post-run on MinKNOW. For more information, please see the MinKNOW protocol.

   5. Click Start to initiate the sequencing run.

2. Duplex basecalling

   Kit 14 chemistry has improved duplex basecalling which requires rebasecalling on Dorado after simplex basecalling has been performed on MinKNOW.

   For detailed information on setting up your sequencing run, for both simplex and duplex basecalling, please see the Kit 14 sequencing and duplex basecalling info sheet.

   Note: When running Dorado, we recommend stopping other basecalling for the best performance by maximising memory available to Dorado. This can be stopped and restarted when Dorado has finished via the GUI on MinKNOW.

3. Data analysis after sequencing

   After sequencing has completed on MinKNOW, the flow cell can be reused or returned, as outlined in the Flow cell reuse and returns section.

   After sequencing and basecalling, the data can be analysed. For further information about options for basecalling and post-basecalling analysis, please refer to the Data Analysis document.

   In the Downstream analysis section, we outline further options for analysing your data.

1. After your sequencing experiment is complete, if you would like to reuse the flow cell, please follow the Flow Cell Wash Kit protocol and store the washed flow cell at +2°C to +8°C.

   The Flow Cell Wash Kit protocol is available on the Nanopore Community.

2. Tip We recommend you to wash the flow cell as soon as possible after you stop the run. However, if this is not possible, leave the flow cell on the device and wash it the next day.
3. Alternatively, follow the returns procedure to send the flow cell back to Oxford Nanopore.

   Instructions for returning flow cells can be found here.

4. Important If you encounter issues or have questions about your sequencing experiment, please refer to the Troubleshooting Guide that can be found in the online version of this protocol.

1. Post-basecalling analysis

   There are several options for further analysing your basecalled data:

   1. EPI2ME workflows

   For in-depth data analysis, Oxford Nanopore Technologies offers a range of bioinformatics tutorials and workflows available in EPI2ME, which are available in the EPI2ME section of the Community. The platform provides a vehicle where workflows deposited in GitHub by our Research and Applications teams can be showcased with descriptive texts, functional bioinformatics code and example data.

   2. Research analysis tools

   Oxford Nanopore Technologies' Research division has created a number of analysis tools, that are available in the Oxford Nanopore GitHub repository. The tools are aimed at advanced users, and contain instructions for how to install and run the software. They are provided as-is, with minimal support.

   3. Community-developed analysis tools

   If a data analysis method for your research question is not provided in any of the resources above, please refer to the resource centre and search for bioinformatics tools for your application. Numerous members of the Nanopore Community have developed their own tools and pipelines for analysing nanopore sequencing data, most of which are available on GitHub. Please be aware that these tools are not supported by Oxford Nanopore Technologies, and are not guaranteed to be compatible with the latest chemistry/software configuration.

1. Below is a list of the most commonly encountered issues, with some suggested causes and solutions.

   We also have an FAQ section available on the Nanopore Community Support section.

   If you have tried our suggested solutions and the issue still persists, please contact Technical Support via email (support@nanoporetech.com) or via LiveChat in the Nanopore Community.

2. Low sample quality

   Observation	Possible cause	Comments and actions
   Low DNA purity (Nanodrop reading for DNA OD 260/280 is <1.8 and OD 260/230 is <2.0–2.2)	The DNA extraction method does not provide the required purity	The effects of contaminants are shown in the Contaminants document. Please try an alternative extraction method that does not result in contaminant carryover. Consider performing an additional SPRI clean-up step.
   Low RNA integrity (RNA integrity number <9.5 RIN, or the rRNA band is shown as a smear on the gel)	The RNA degraded during extraction	Try a different RNA extraction method. For more info on RIN, please see the RNA Integrity Number document. Further information can be found in the DNA/RNA Handling page.
   RNA has a shorter than expected fragment length	The RNA degraded during extraction	Try a different RNA extraction method. For more info on RIN, please see the RNA Integrity Number document. Further information can be found in the DNA/RNA Handling page. We recommend working in an RNase-free environment, and to keep your lab equipment RNase-free when working with RNA.

3. Low DNA recovery after AMPure bead clean-up

   Observation	Possible cause	Comments and actions
   Low recovery	DNA loss due to a lower than intended AMPure beads-to-sample ratio	1. AMPure beads settle quickly, so ensure they are well resuspended before adding them to the sample. 2. When the AMPure beads-to-sample ratio is lower than 0.4:1, DNA fragments of any size will be lost during the clean-up.
   Low recovery	DNA fragments are shorter than expected	The lower the AMPure beads-to-sample ratio, the more stringent the selection against short fragments. Please always determine the input DNA length on an agarose gel (or other gel electrophoresis methods) and then calculate the appropriate amount of AMPure beads to use.
   Low recovery after end-prep	The wash step used ethanol <70%	DNA will be eluted from the beads when using ethanol <70%. Make sure to use the correct percentage.

1. Below is a list of the most commonly encountered issues, with some suggested causes and solutions.

   We also have an FAQ section available on the Nanopore Community Support section.

   If you have tried our suggested solutions and the issue still persists, please contact Technical Support via email (support@nanoporetech.com) or via LiveChat in the Nanopore Community.

2. Fewer pores at the start of sequencing than after Flow Cell Check

   Observation	Possible cause	Comments and actions
   MinKNOW reported a lower number of pores at the start of sequencing than the number reported by the Flow Cell Check	An air bubble was introduced into the nanopore array	After the Flow Cell Check it is essential to remove any air bubbles near the priming port before priming the flow cell. If not removed, the air bubble can travel to the nanopore array and irreversibly damage the nanopores that have been exposed to air. The best practice to prevent this from happening is demonstrated in this video.
   MinKNOW reported a lower number of pores at the start of sequencing than the number reported by the Flow Cell Check	The flow cell is not correctly inserted into the device	Stop the sequencing run, remove the flow cell from the sequencing device and insert it again, checking that the flow cell is firmly seated in the device and that it has reached the target temperature. If applicable, try a different position on the device (GridION/PromethION).
   MinKNOW reported a lower number of pores at the start of sequencing than the number reported by the Flow Cell Check	Contaminations in the library damaged or blocked the pores	The pore count during the Flow Cell Check is performed using the QC DNA molecules present in the flow cell storage buffer. At the start of sequencing, the library itself is used to estimate the number of active pores. Because of this, variability of about 10% in the number of pores is expected. A significantly lower pore count reported at the start of sequencing can be due to contaminants in the library that have damaged the membranes or blocked the pores. Alternative DNA/RNA extraction or purification methods may be needed to improve the purity of the input material. The effects of contaminants are shown in the Contaminants Know-how piece. Please try an alternative extraction method that does not result in contaminant carryover.

3. MinKNOW script failed

   Observation	Possible cause	Comments and actions
   MinKNOW shows "Script failed"		Restart the computer and then restart MinKNOW. If the issue persists, please collect the MinKNOW log files and contact Technical Support. If you do not have another sequencing device available, we recommend storing the flow cell and the loaded library at 4°C and contact Technical Support for further storage guidance.

4. Pore occupancy below 40%

   Observation	Possible cause	Comments and actions
   Pore occupancy <40%	Not enough library was loaded on the flow cell	Ensure the correct volume and concentration as stated on the appropriate protocol for your sequencing library is loaded onto the flow cell. Please quantify the library before loading and calculate fmols using tools like the Promega Biomath Calculator, choosing "dsDNA: µg to fmol"
   Pore occupancy close to 0	The Ligation Sequencing Kit was used, and sequencing adapters did not ligate to the DNA	Make sure to use the NEBNext Quick Ligation Module (E6056) and Oxford Nanopore Technologies Ligation Buffer (LNB, provided in the sequencing kit) at the sequencing adapter ligation step, and use the correct amount of each reagent. A Lambda control library can be prepared to test the integrity of the third-party reagents.
   Pore occupancy close to 0	The Ligation Sequencing Kit was used, and ethanol was used instead of LFB or SFB at the wash step after sequencing adapter ligation	Ethanol can denature the motor protein on the sequencing adapters. Make sure the LFB or SFB buffer was used after ligation of sequencing adapters.
   Pore occupancy close to 0	No tether on the flow cell	Tethers are adding during flow cell priming (FLT tube for Kit 9, 10, 11, FCT for Kit 14, and FTU for ultra-long DNA kits). Make sure FLT/FCT/FTU was added to the buffer (FB for Kit 9, 10, 11, and FCF for Kit 14) before priming.

5. Shorter than expected read length

   Observation	Possible cause	Comments and actions
   Shorter than expected read length	Unwanted fragmentation of DNA sample	Read length reflects input DNA fragment length. Input DNA can be fragmented during extraction and library prep. 1. Please review the Extraction Methods in the Nanopore Community for best practice for extraction. 2. Visualise the input DNA fragment length distribution on an agarose gel before proceeding to the library prep. In the image above, Sample 1 is of high molecular weight, whereas Sample 2 has been fragmented. 3. During library prep, avoid pipetting and vortexing when mixing reagents. Flicking or inverting the tube is sufficient.

6. Large proportion of unavailable pores

   Observation	Possible cause	Comments and actions
   Large proportion of unavailable pores (shown as blue in the channels panel and pore activity plot) The pore activity plot above shows an increasing proportion of "unavailable" pores over time.	Contaminants are present in the sample	Some contaminants can be cleared from the pores by the unblocking function built into MinKNOW. If this is successful, the pore status will change to "sequencing pore". If the portion of unavailable pores stays large or increases: 1. A nuclease flush using the Flow Cell Wash Kit (EXP-WSH004) can be performed, or 2. Run several cycles of PCR to try and dilute any contaminants that may be causing problems.

7. Large proportion of inactive pores

   Observation	Possible cause	Comments and actions
   Large proportion of inactive/unavailable pores (shown as light blue in the channels panel and pore activity plot. Pores or membranes are irreversibly damaged)	Air bubbles have been introduced into the flow cell	Air bubbles introduced through flow cell priming and library loading can irreversibly damage the pores. Watch the Priming and loading your flow cell video for best practice
   Large proportion of inactive/unavailable pores	Certain compounds co-purified with DNA	Known compounds, include polysaccharides, typically associate with plant genomic DNA. 1. Please refer to the Plant leaf DNA extraction method. 2. Clean-up using the QIAGEN PowerClean Pro kit. 3. Perform a whole genome amplification with the original gDNA sample using the QIAGEN REPLI-g kit.
   Large proportion of inactive/unavailable pores	Contaminants are present in the sample	The effects of contaminants are shown in the Contaminants Know-how piece. Please try an alternative extraction method that does not result in contaminant carryover.

8. Temperature fluctuation

   Observation	Possible cause	Comments and actions
   Temperature fluctuation	The flow cell has lost contact with the device	Check that there is a heat pad covering the metal plate on the back of the flow cell. Re-insert the flow cell and press it down to make sure the connector pins are firmly in contact with the device. If the problem persists, please contact Technical Services.

9. Failed to reach target temperature

   Observation	Possible cause	Comments and actions
   MinKNOW shows "Failed to reach target temperature"	The instrument was placed in a location that is colder than normal room temperature, or a location with poor ventilation (which leads to the flow cells overheating)	MinKNOW has a default timeframe for the flow cell to reach the target temperature. Once the timeframe is exceeded, an error message will appear and the sequencing experiment will continue. However, sequencing at an incorrect temperature may lead to a decrease in throughput and lower q-scores. Please adjust the location of the sequencing device to ensure that it is placed at room temperature with good ventilation, then re-start the process in MinKNOW. Please refer to this link for more information on MinION temperature control.