CRUK-CI Genomics Help

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submission:slx_submissions [2025/09/29 15:57] – [Submission Guidelines] Johanna Barbierisubmission:slx_submissions [2026/08/04 15:15] (current) – [Submission Guidelines] 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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            * **Index** must be the corresponding Index Name (e.g. i701_i501) rather than the index sequence. Some index types are grouped (for instance all Nextera kits as they all use the same original set of Illumina Nextera index sequence), so as long as the sequence matches your index sequence you are able to submit using that index name.            * **Index** must be the corresponding Index Name (e.g. i701_i501) rather than the index sequence. Some index types are grouped (for instance all Nextera kits as they all use the same original set of Illumina Nextera index sequence), so as long as the sequence matches your index sequence you are able to submit using that index name.
            * **Species** is only needed if you have a mix of species in the pool. Use this field to assign a species for any sample whose species differs from that set in cell C25 (the species common across the pool).            * **Species** is only needed if you have a mix of species in the pool. Use this field to assign a species for any sample whose species differs from that set in cell C25 (the species common across the pool).
-  - For a pool with no indexing, inline barcodes or unspecified indexing, complete a single row for the whole pool; i.e. a pool of six libraries is still only one row in the sample information table. The index should read //"None"// for no index, //"INLINE"// for inline barcodes and //"Unspecified Index"// for custom indexing. As noted in point 2, the number of samples in pool should be set to 1.+  - For a pool with no indexing, inline barcodes or unspecified indexing, complete a single row for the whole pool; i.e. a pool of six libraries is still only one row in the sample information table. The index should read //"No Index"// for no index, //"INLINE"// for inline barcodes and //"Unspecified Index"// for custom indexing. As noted in point 2, the number of samples in pool should be set to 1.
  
 A full list of the supported indexes can be found on the index information page. If your index type is not currently supported, email the genomics helpdesk to enquire if the new indexes could be added. We cannot add every available index, but we will add to our list if there is a significant requirement for new indexing kits or options. A full list of the supported indexes can be found on the index information page. If your index type is not currently supported, email the genomics helpdesk to enquire if the new indexes could be added. We cannot add every available index, but we will add to our list if there is a significant requirement for new indexing kits or options.
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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.
-           * MiSeq Express: 15µl at 4nM precisely.+           * NextSeq: 15µl of your pooled library at 10-20nM. 
 +           * MiSeq Express or NextSeq Express: 15µl at 4nM precisely.
            * NovaSeq submissions dependent upon flowcell type:            * NovaSeq submissions dependent upon flowcell type:
  
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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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 | ^MiSeq |^NextSeq 2000 |||^MiSeq i100||^NovaSeq X Plus ^|| | ^MiSeq |^NextSeq 2000 |||^MiSeq i100||^NovaSeq X Plus ^||
-| |Standard (M) | Nano (M) | P1 (M) | P2 (M) | P3 (B) | P4 (B)| 5M (M) | 25M (M) || 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|1.8|5 | 25|| 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| 6 | 25 || 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% | 
-| All other library types | 5% | 1% | 2% |+| All other library types | 5% | 2% | 2% |
 * Optimisation may be required. * Optimisation may be required.