DRAGEN NextSeq 2000 Sequencing Systems
លក្ខណៈបច្ចេកទេស
- Product Name: DRAGEN Single Cell RNA v4.2.11 for NextSeq 1000/2000
- លេខផ្នែក : N/A
- លេខឯកសារ៖ 200074785
- កំណែ៖ 00
- Effective Date: 19-Sep-2025 04:33 to UP (NONE)
ការណែនាំ
These Release Notes detail the key changes to the DRAGEN Single Cell RNA Workflow onboard the NextSeq 1000/2000 instrument, since the v4.2.7 release. If you are updating from an older version, please see all intermediate release notes.
CHANGES IN V4.2.11
- scRNA Analysis
- Fixed issue where Fastq List Import incorrectly handles empty R1
- On-instrument Specific
- Add support for the Oracle9 OS
- Robustness improvements for on-board analyses, and fix for a potential deadlock
- Fixed a pre-run validation error when Ora compression is specified but no FASTQs are to be kept
- Fixed a log rotation bug that caused logs to accumulate on the instrument
- Remove R and Rscript dependencies from the installer, to resolve a cybersecurity finding.
កំណត់ចំណាំ
Reference Genome Usage Recommendations
Germline, Enrichment Germline, Amplicon Germline Workflows
- Use ALT-Masked mapping.
- Use Graph genomes.
- Use the Homo sapiens [1000 Genomes] hg38 Alt Masked Graph v3 reference genome.
- If not using hg38, the Homo sapiens [UCSC] hg19 Alt Masked Graph v3 or Homo sapiens [NCBI] hs37d5 v3 Graph are recommended.
- Non-graph is supported, but has reduced accuracy
Enrichment Somatic, Amplicon Somatic, RNA and scRNA Workflows
- Use ALT-Masked mapping.
- Use non-Graph genomes.
- Use the Homo sapiens [1000 Genomes] hg38 Alt Masked v3 reference genome or Homo sapiens [UCSC] hg19 Alt Masked v3 reference genome.
Table 1 v4.2 Reference Support and Recommended Use for Human Data
| មនុស្ស | hg19 | hs37d5 | hg38 | chm13 | Recommended Reference Type | |
|
Germline |
SNV | បាទ | បាទ | បាទ | បាទ | ក្រាហ្វ |
| CNV | បាទ | បាទ | បាទ | បាទ* | ក្រាហ្វ | |
| SV | បាទ | បាទ | បាទ | បាទ* | ក្រាហ្វ | |
| Expansion Hunter | បាទ | បាទ | បាទ | ទេ | ក្រាហ្វ |
| អ្នកហៅចូលគោលដៅ | បាទ | បាទ | បាទ | ទេ | ក្រាហ្វ | |
| RNA | បាទ | បាទ | បាទ | បាទ* | Non-Graph | |
| De Novo | បាទ | បាទ | បាទ | បាទ* | ក្រាហ្វ | |
| ការធ្វើ Genotyping រួម | បាទ | បាទ | បាទ | បាទ* | ក្រាហ្វ | |
| Biomarkers (HLA) | បាទ | បាទ | បាទ | បាទ* | ក្រាហ្វ | |
| Gvcf Genotyper | បាទ | បាទ | បាទ | បាទ* | ក្រាហ្វ | |
|
Somatic |
SNV | បាទ | បាទ | បាទ | បាទ* | Non-Graph |
| UMI SNV | បាទ | បាទ | បាទ | បាទ* | Non-Graph | |
| CNV | បាទ | បាទ | បាទ | បាទ* | Non-Graph | |
| SV | បាទ | បាទ | បាទ | បាទ* | Non-Graph | |
| មេទីល | មេទីល | បាទ | បាទ | បាទ | ទេ | Non-Graph |
| ចំណារពន្យល់ | និព្វាន | បាទ | បាទ | បាទ | ទេ | ន/ក |
(*) DRAGEN™ supports the component execution; however, the component’s accuracy has not been established.
Table 2 v4.2 Reference Support and Recommended Use for Non-Human Data Non-Human
| មិនមែនមនុស្ស | គាំទ្រ | Recommended Reference Type | |
|
Germline |
SNV | បាទ | Non-Graph |
| CNV | ទេ | ន/ក | |
| SV | បាទ | Non-Graph | |
| Expansion Hunter | ទេ | ន/ក | |
| អ្នកហៅចូលគោលដៅ | ទេ | ន/ក | |
| RNA | បាទ | Non-Graph | |
| De Novo | បាទ | Non-Graph | |
| ការធ្វើ Genotyping រួម | បាទ | Non-Graph | |
| Biomarkers (HLA) | ទេ | ន/ក | |
| Gvcf Genotyper | បាទ | Non-Graph | |
|
Somatic |
SNV | ទេ | ន/ក |
| UMI SNV | ទេ | ន/ក | |
| CNV | ទេ | ន/ក | |
| SV | ទេ | ន/ក | |
| មេទីល | មេទីល | ទេ | ន/ក |
| ចំណារពន្យល់ | និព្វាន | បាទ | ន/ក |
How to Update Instrument Reference Genomes
You can only import new reference genomes from the administrator account.
ជំហាន៖
- Download the desired genome package tar.gz from the NextSeq 1000/2000 Software Downloads page, OR
- Create a reference genome using the Reference Builder for Illumina Instruments BaseSpace Sequence Hub app. For more information, refer to Reference Builder for Illumina Instruments v1.0.0 App Online Help.
- Select the control software menu, and then select Process Management. Make sure that there are no sequencing runs or on-instrument secondary analyses in progress.
- From the control software menu, select Minimize Application.
- Log into ilmnadmin.
- Select the control software menu, and then select DRAGEN.
- In the Genome section, select View Installed Genomes to view a list of all currently installed genomes.
- បិទបង្អួច។
- Under Import New Reference Genomes, select Choose.
Navigate to the reference genome file (*.tar.gz) on the portable or mounted network drive, and then select Open.
បញ្ហាដែលបានជួសជុល
Fixed issues of the DRAGEN™ v4.2.11 Single Cell RNA Workflow
| សមាសភាគ | លេខសម្គាល់ពិការភាព | ការពិពណ៌នាបញ្ហា |
| scRNA | DRAGEN- ១៤២៧៤ | Fix for Single cell scRNA.barcodeSummary.csv reporting incorrect UMI counts |
| scRNA | DRAGEN– 24741 | Fix to allow pre-signed URLs for UMI files in FASTQ list.csv |
|
ស្កាតាក |
DRAGEN- 22854, SET-
4565 |
Fix for Feature/Peak ID missing in scRNA/scATAC output |
| QC Metrics, scRNA | DRAGEN- ១៤២៧៤ | Fix a run-to-run variation in scRNA on bdbio |
| scRNA | DRAGEN- ១៤២៧៤ | Fix for DRAGEN on NextSeq 2000: Single Cell RNA hang-up |
| scRNA | DRAGEN- ១៤២៧៤ | Fix the number of non-null entries in the matrix.mtx file (feature counting) |
ការណែនាំអំពីការដំឡើង
DRAGEN v4.2.11 workflows are compatible with Control Software 2.0.x. For information regarding compatibility with other Control Software versions, please reference the NextSeq 1000/2000 Compatible Products page on the Illumina support site. If you would like to update the control software, please follow the steps detailed in the NextSeq 1000/2000 Control Software Suite v2.0.x Release Notes on the Illumina Support Site.
Online Installation of Workflows
If the instrument is connected to the internet, you can install DRAGEN workflows directly from the Control Software. Online installation of workflows is available since Control Software v1.3 or later.
ជំហាន៖
- ត្រូវប្រាកដថាអ្នកមានពាក្យសម្ងាត់ទៅកាន់គណនី ilmnadmin ។
- ចូលទៅគណនី ilmnadmin៖
- a. If you are logged in as ilmnuser and in control software, select the control software menu, and then select Exit Application to access the desktop.
- ខ. ជ្រើសរើសរូបតំណាងប៊ូតុងថាមពលនៅជ្រុងខាងស្តាំខាងលើ ហើយចេញពី ilmnuser ។
- គ. បន្ទាប់ពីអ្នកនៅលើអេក្រង់ចូល សូមជ្រើសរើស ilmnadmin ហើយបន្ទាប់មកបញ្ចូលពាក្យសម្ងាត់ដើម្បីចូល។
- ឃ. កម្មវិធីគ្រប់គ្រងនឹងបើកដំណើរការដោយស្វ័យប្រវត្តិនៅពេលអ្នកចូល។
- Make sure that there are no sequencing runs or on-instrument secondary analysis in progress.
- On the control software menu, select DRAGEN. Under Version, the Available Workflows section lists the workflows currently installed on the system.
- Select Check Online. Not all DRAGEN versions and workflows are compatible with online installation. Use offline installation for additional workflows.
- Select the checkbox for the workflows that you would like to install. NOTE: For Online Updates, DRAGEN BCL Convert must be installed before or with other workflows of the same DRAGEN Version. You can view information about the latest version of a workflow in the release notes.
- Select Install to start installation.
- Enter ilmnadmin for the system password, and then select Authenticate.
- បន្ទាប់ពីការដំឡើងបានបញ្ចប់ អ្នកនឹងត្រូវបានរុករកត្រឡប់ទៅអេក្រង់ DRAGEN ហើយអាច view បញ្ជីដែលបានធ្វើបច្ចុប្បន្នភាពនៃដំណើរការការងារ DRAGEN ដែលបានដំឡើង។
Offline Installation of Workflows
ជំហាន៖
- When a DRAGEN workflow update is available, download the installer (*.tar.gz) from the NextSeq 1000/2000 Sequencing System support page. Save the installer to a local or portable drive. Note: at minimum, you must download and install the DRAGEN BCL Convert update of the same DRAGEN Version.
- If you saved the installer to a portable drive, plug the drive into a USB 3.0 port, located on both the side and back of the instrument. Gently move the instrument as needed to access the back.
- Follow steps 1-3 above to log in to ilmnadmin.
- Select the control software menu, and then select DRAGEN.
- Under Version, select Browse for New Version to navigate to the installer. Note: DRAGEN BCL Convert of the same DRAGEN Version must be installed before other workflows.
- Select Install to start installation.
- Enter ilmnadmin for the system password, and then select Authenticate.
- បន្ទាប់ពីការដំឡើងបានបញ្ចប់ អ្នកនឹងត្រូវបានរុករកត្រឡប់ទៅអេក្រង់ DRAGEN ហើយអាច view បញ្ជីដែលបានធ្វើបច្ចុប្បន្នភាពនៃដំណើរការការងារ DRAGEN ដែលបានដំឡើង។
Note that starting with control software v1.5, it is possible to uninstall previous versions of DRAGEN workflows.
ចេញផ្សាយប្រវត្តិសាស្ត្រ
| ការពិនិត្យឡើងវិញ | ការចេញផ្សាយឯកសារយោង | អ្នកបង្កើត | ការពិពណ៌នាអំពីការផ្លាស់ប្តូរ |
| 00 | CN ២០ | Seth Gwin | ការចេញផ្សាយដំបូង |
ទំនាក់ទំនង
- Title: DRAGEN Single Cell RNA v4.2.11 for NextSeq 1000/2000 Customer Release Notes
- លេខផ្នែក : N/A
- លេខឯកសារ៖ 200074785, កំណែ: 00
- Effective Date: 19-Sep-2025 04:33 to UP (NONE)
សំណួរគេសួរញឹកញាប់
Q: How often should I update the reference genomes on the instrument?
A: It is recommended to update the reference genomes whenever a new version is released to ensure compatibility and optimal performance.
Q: What should I do if I encounter a pre-run validation error?
A: If you face a pre-run validation error, ensure that the Ora compression is specified correctly and check if the required FASTQs are available. If the issue persists, refer to the troubleshooting section of the manual.
ឯកសារ/ធនធាន
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DRAGEN NextSeq 2000 Sequencing Systems [pdf] សៀវភៅណែនាំ NextSeq 1000, NextSeq 2000, NextSeq 2000 Sequencing Systems, Sequencing Systems, Systems |