CRUK-CI Genomics Help

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submission:slx_submissions [2025/09/30 08:40] – [Complete the Pool Information Fields] Johanna Barbierisubmission:slx_submissions [2026/03/13 14:42] (current) – [Submission Guidelines] Johanna Barbieri
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   -  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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   - 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__.
  
  
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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:
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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.