CRUK-CI Genomics Help

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submission:slx_submissions [2025/02/10 13:39] – [Yields] Johanna Barbierisubmission:slx_submissions [2026/05/15 13:10] (current) – [Further information] Johanna Barbieri
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   -  Enter the **number of samples in the pool** to be sequenced. If this is a pool without multiplexing, or a pool with in-line barcodes or custom indexing, set the pool size to 1.   -  Enter the **number of samples in the pool** to be sequenced. If this is a pool without multiplexing, or a pool with in-line barcodes or custom indexing, set the pool size to 1.
   -  Choose a sequencing **workflow**:   -  Choose a sequencing **workflow**:
-           * //NovaSeqX or NovaSeq 6000//: use this for direct NovaSeq sequencing requests. +           * //NovaSeqX //: use this for direct NovaSeq sequencing requests. 
-           *  //NovaSeq (X or 6000) with MiSeq Nano QC//: use this for NovaSeq sequencing requests which include a MiSeq Nano validation run of your library pool first; this provides an opportunity to adjust your pool if required before committing to the NovaSeq flowcell. This is highly recommended if you want to run multiple lanes of sequencing.+           *  //NovaSeq X with MiSeq Nano QC//: use this for NovaSeq sequencing requests which include a MiSeq Nano validation run of your library pool first; this provides an opportunity to adjust your pool if required before committing to the NovaSeq flowcell. This is highly recommended if you want to run multiple lanes of sequencing.
            * //MiSeq//: use this for all standard MiSeq v3 sequencing requests.            * //MiSeq//: use this for all standard MiSeq v3 sequencing requests.
            * //MiSeq Express//: use this for MiSeq v3 sequencing if you want us to use your quantified concentration. We ask for samples to be submitted at 4nM and will not quantify your library ourselves.            * //MiSeq Express//: use this for MiSeq v3 sequencing if you want us to use your quantified concentration. We ask for samples to be submitted at 4nM and will not quantify your library ourselves.
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   -  Select **read length** from the drop-down menu or enter it manually if it is asymmetrical (e.g. 92+26).   -  Select **read length** from the drop-down menu or enter it manually if it is asymmetrical (e.g. 92+26).
   -  Enter the **number of lanes** required. See table 2 below for expected yields for each flowcell type.   -  Enter the **number of lanes** required. See table 2 below for expected yields for each flowcell type.
-  -  For NovaSeq and NextSeq 2000 runs, select the flowcell type.\\ The NovaSeq6000 flowcells are the "S" ones (SP, S1, S2, S4); the NextSeq 2000 flowcells are the "P" ones (P1, P2, P3); The NovaSeq X flowcells are the “B” ones (1.5B, 10B, 25B).\\  Leave this field empty for other sequencers.+  -  For NovaSeq and NextSeq 2000 runs, select the flowcell type.\\ The NextSeq 2000 flowcells are the "P" ones (P1, P2, P3); The NovaSeq X flowcells are the “B” ones (1.5B, 10B, 25B).\\  Leave this field empty for other sequencers.
   -  Select library type from the drop-down menu.\\  //Important: if submitting for the library types "Amplicon low diversity", "Amplicon high diversity" or "Bisulphite" please read table 3 below regarding PhiX spike-in percentage.//   -  Select library type from the drop-down menu.\\  //Important: if submitting for the library types "Amplicon low diversity", "Amplicon high diversity" or "Bisulphite" please read table 3 below regarding PhiX spike-in percentage.//
   -  If you are submitting for unspecified indexing where you will demultiplex yourself, you must specify the **index lengths** required for each index. _We cannot accept your library unless we have this information_.   -  If you are submitting for unspecified indexing where you will demultiplex yourself, you must specify the **index lengths** required for each index. _We cannot accept your library unless we have this information_.
   -  Enter the average library length including insert and adapters (see point 4 of further information).   -  Enter the average library length including insert and adapters (see point 4 of further information).
-  -  Select required option for **custom primers**. See the custom primers guide for more information.+  -  Select required option for **custom primers**. See the**[[customprimers| custom primers guide]]** for more information.
   -  Select **sample type, sample source and species** from the drop down menus.   -  Select **sample type, sample source and species** from the drop down menus.
   -  Complete **billing information**. This is critical for correct invoicing: please follow the popup instructions in the field. Only enter a **PO number** if applicable to your department or organisation. **Leave PO number blank if it does not apply!** Resist the temptation to put "N/A" or "None": it will complicate your bills.   -  Complete **billing information**. This is critical for correct invoicing: please follow the popup instructions in the field. Only enter a **PO number** if applicable to your department or organisation. **Leave PO number blank if it does not apply!** Resist the temptation to put "N/A" or "None": it will complicate your bills.
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 ==== Make the Submission ==== ==== Make the Submission ====
  
-  - Run your completed submission form through this submission application. Any errors will be reported back to you for correction. If there are no errors, you will be asked to confirm your submission to the Genomics' LIMS system.+  - Run your completed submission form through this [[https://genomicsequencing.cruk.cam.ac.uk/sequencing/submit/UploadSubmission.action|submission application]]. Any errors will be reported back to you for correction. If there are no errors, you will be asked to confirm your submission to the Genomics' LIMS system.
   - Once your submission is complete, bring your SLX tube(s) to Genomics lab 026 or the Cambridge Institute reception for our external collaborators. Reception can accept tubes between 09:30-16:30 Monday to Friday.   - Once your submission is complete, bring your SLX tube(s) to Genomics lab 026 or the Cambridge Institute reception for our external collaborators. Reception can accept tubes between 09:30-16:30 Monday to Friday.
  
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   - We strongly recommend that you do not mix barcoding kits (index types) in the same pool. We cannot demultiplex such pools and there is a risk of using barcodes too similar to each other for demultiplexing to separate.   - We strongly recommend that you do not mix barcoding kits (index types) in the same pool. We cannot demultiplex such pools and there is a risk of using barcodes too similar to each other for demultiplexing to separate.
   - If you must submit a pool with two or more different barcoding kits used in it, please submit with Index Type set to "Unspecified (Other)". The pool can be sequenced to your requirements but it is wholly your responsibility to demultiplex the FASTQ files you will receive. The sequencing service does not support demultiplexing such pools.   - If you must submit a pool with two or more different barcoding kits used in it, please submit with Index Type set to "Unspecified (Other)". The pool can be sequenced to your requirements but it is wholly your responsibility to demultiplex the FASTQ files you will receive. The sequencing service does not support demultiplexing such pools.
-  - If you submit a sample for **multiple lanes** of NovaSeq, **__we strongly suggest running a MiSeq nano__** to help us optimise loading on the instrument. Failing that, __we can't guaranty optimal results__.+  - If you submit a sample for **multiple lanes** of NovaSeq X, **__we strongly suggest running a MiSeq i100__** to help us optimise loading on the instrument. Failing that, __we can't guaranty optimal results__. 
 +  - Please bear in mind that the size of sequencing data can be very large (especially for multiple lanes of NovaSeq X 25B). Make sure you have enough space set aside to download the data.
  
  
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            * MiSeq: 15µl of your pooled library at 10-20nM.            * MiSeq: 15µl of your pooled library at 10-20nM.
 +           * NextSeq: 15µl of your pooled library at 10-20nM.
            * MiSeq Express: 15µl at 4nM precisely.            * MiSeq Express: 15µl at 4nM precisely.
            * NovaSeq submissions dependent upon flowcell type:            * NovaSeq submissions dependent upon flowcell type:
  
-**Table 1 - NovaSeq 6000 submission requirements (library volume)** 
-^Flowcell type ^Concentration range ^Min Volume per lane, Xp workflow ^Min Volume per flowcell, Standard workflow^ 
-|NovaSeq S1&S1 | 5-10nM |20µl |50µl | 
-|NovaSeq S2 | 5-10nM |25µl |75µl | 
-|NovaSeq S4 | 5-10nM |30µl |200µl | 
  
-The Xp workflow is used when you submit a single lane or less than an entire flowcell. The Standard workflow is used when you submit for an entire flowcell (i.e. two lanes for SP, S1 and S2 flowcells, and four lanes for S4 flowcells). +**Table 1 - NovaSeq X Plus submission requirements (library volume)**
- +
-**Table 2 - NovaSeq X Plus submission requirements (library volume)**+
 ^Flowcell type ^Concentration range ^Min Volume per lane^ ^Flowcell type ^Concentration range ^Min Volume per lane^
 |NovaSeq X 1.5B | 5-10nM |20µl | |NovaSeq X 1.5B | 5-10nM |20µl |
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 |NovaSeq X 25B | 5-10nM |30µl | |NovaSeq X 25B | 5-10nM |30µl |
  
-There is no standard workflow available, like on the NovaSeq 6000, only “Xp”.+Please do not submit molarities above 50nM.
  
 ==== Yields ==== ==== Yields ====
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 **Table 3 - Reads per lane** **Table 3 - Reads per lane**
  
-| ^MiSeq |^NextSeq 2000 |||^NovaSeq 6000||||^NovaSeq X Plus ^|| +| ^MiSeq |^NextSeq 2000 |||^MiSeq i100||^NovaSeq X Plus ^|| 
-| |Standard (M) | Nano (M) | P1 (M) | P2 (M) | P3 (B) | P4 (B)| SP (M) | S1 (M) | S2 (B) | S4 (B) || 1.5B (M) | 10B (B) | 25B (B)| +| |Standard (M) | Nano (M) | P1 (M) | P2 (M) | P3 (B) | P4 (B)| 5M (M) | 25M (M) || 1.5B (B) | 10B (B) | 25B (B)| 
-^Specifications | 15-25 | 1 |100|400|1.2|1.8Z|325-400 | 650-800 | 1.65-2.05 | 2-2.5 || 750 | 1.25 | 3.125 | +^Specifications | 15-25 | 1 |100|400|1.2|1.8|5 | 25|| 0.750 | 1.25 | 3.125 | 
-^ Typical performance | 15-28 | ≤1 | 100 | 400|1.2|1.8| 500 | 950 | 2 | 2.7-3 || 1000| 1.25 | 3.125 |+^ Typical performance | 15-28 | ≤1 | 100 | 400|1.2|1.8| 6 | 25 || 1| 1.4| 3.9 | 
  
  
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-^Library type ^MiSeq ^NovaSeq 6000 ^NovaSeq X Plus | +^Library type ^MiSeq ^MiSeq i100 ^NovaSeq X Plus | 
-|Bisulphite Converted | 5% | ≥5%* | ≥5%* | +|Bisulphite Converted | 5% | 5%* | ≥5%* | 
-|Amplicon Low-Diversity | 10% | ≥5%* | 10-20%* | +|Amplicon Low-Diversity | 10% | 5%* | 10-20%* | 
-|Amplicon High-Diversity | 5% | 1% | 1% | +|Amplicon High-Diversity | 5% | 2% | 2% | 
-|mRNA (A/T ligation library) | 1% | 1% | 10%* |  +| All other library types | 5% | 2% | 2% |
-| All other library types | 5% | 1% | 1% |+
 * Optimisation may be required. * Optimisation may be required.