Nextseq sample sheet To save the run configuration as a sample sheet in v2 file format, select Export. This ensures that the Sample Sheet is configured correctly to prevent errors with run setup or Analysis. Every run in BaseSpace Sequence Hub requires an associated sample sheet to define projects and samples, assign indexes, and run workflow apps. Take the guesswork out of your next workflow. If you would like reverse complement sequences to be included in your sample sheet, use the BCL2FASTQ_Reverse_Complement_Samplesheet. When output exceeds specifications, the real- world cost per sample decreases. The default configuration for the Illumina NextSeq integration is shown below. All NextSeq 550 System kits are paired-end capable. Detailed Steps for Run The selected sample sheet must be in v2 format. Make sure any files referenced in the sample sheet Generates the sample sheet and attaches it to the placeholder in the Files area of the Record Details screen for all Run Mode types. The tool handles demultiplexing and conversion of the BCL base-call files output by the NextSeq instrument into FastQ files used by many third-party analysis platforms. Sample Sheet templates for TSO 500 standalone DRAGEN server and ICA manual launch analysis can be found in the table below. View output, run time, reads passing filter, sample throughput, and other key specifications for the NextSeq 1000 and NextSeq 2000 Sequencing Systems. Refer to ICA Auto-launch Sample Sheet Requirements for The NextSeq 1000/2000 Control Software will validate the Sample Sheet used to setup a sequencing run or DRAGEN analysis. Download Sample Sheet v2 Template here. The file includes a list of samples, their index sequences, and the sequencing workflow. Make sure any files referenced in the sample sheet Jan 7, 2025 路 When demultiplexing, the final sample sheet provided to the FASTQ generation software needs to have the i5 index in the correct orientation for that platform. However, DRAGEN will automatically reverse complement i5 indexes from v2 sample sheets. Filling out the form on the user interface will produce a exportable sample sheet with the required fields filled in. csv) file format used by Illumina instruments, platforms, and analysis pipelines to store settings and data for sequencing and analysis. Use the Workflow B template for the iSeq 100, HiSeq 3000, HiSeq 4000, HiSeq X, MiniSeq, NextSeq 500, or NextSeq 550 Systems. Use the Worklow A template for the HiSeq 2000, HiSeq 2500, MiSeq, or NovaSeq 6000 Systems. Run Set Up Sample Sheet Index Orientation Guide i5 Index Orientation Table This table describes how to enter the i5 sequence, Forward (F) or Reverse Complement (RC), depending on the instrument and software used. For more details, see Import Samples. Use Illumina Mar 25, 2025 路 In this example, the NextSeq 2000 is compatible with a v2 sample sheet from Illumina’s run setup software. Sample Sheet Generation Sample sheet generation occurs on the step before the sequencing run Denature and Dilute (NextSeq 500/550 v1. To create a sample sheet v2, download the generated sample sheet from Run Planning in BaseSpace Sequence Hub or edit a sample sheet v2 template provided on the NextSeq 1000/2000 support page. For more information on sample sheet v2 format and requirements, refer to the Sample Sheet v2 Resource. zip folder, and are required to initiate runs on systems using Local mode. If Sample Sheet is selected, make sure that your sample sheet meets the formatting requirements. Use the following steps to find the log file for the sample sheet: Mar 10, 2010 路 Copy Run Set Up Sample Sheet Intrument Settings NextSeq 1000/2000 Settings NextSeq 1000/2000 Sample Sheet Version History = Supported 馃煥 = Supported. This option is only available if Local was selected for analysis location. See Release Notes and/or Sample Sheet Definition for each version for details. Follow the guidance in the Sample Sheet v2 Resource NextSeq 1000/2000 Settings. The next step is AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing v2. Jan 16, 2018 路 A custom product file for use with IDT for Illumina TruSeq UD Indexes and the Illumina Experiment Manager (IEM) software. The sample sheet and secondary analysis supporting files are downloaded in a *. The BaseSpace Sequence Hub Run Planning tool is available and is used to generate a valid sample sheet in v2 format for use on a TSO 500 supported sequencer for both ICA and Standalone DRAGEN Server analysis options. On the Assign Next Steps screen, the next step for samples is set to the next step in the workflow. Apr 25, 2016 路 The sample sheet file should resemble the example below – this is for a paired end 2x151bp NextSeq run with four samples, TruSeqLT index tags, and adapter trimming selected. However, most Illumina sample sheet generation software handles this automatically. The sample sheet can be placed on the NextSeq 1000/2000 instrument or remain on the portable/mounted drive. The NextSeq 1000/2000 uses the reverse complement workflow indexing strategy. csv) files with Illumina instruments, platforms, and analysis pipelines, refer to the Sample Sheet v2 Resources support page. The sample sheet can be placed on the NextSeq 1000/2000 instrument or remain on the portable/mounted drive. Sample Sheet v2 Resources For information on using v2 sample sheet (*. Historically, v1 sample sheets for reverse complement workflow indexing strategy instrument required the i5 index sequence in the reverse complement orientation. If CSV is selected, make sure to use the correct template as the template can be different depending on the selected index adapter kit and index strategy. This miniaturization provides scalability for various output quantities while maintaining the same high standards of data quality as a. Blank = Not supported The forward strand workflow is performed on the NovaSeq 6000, MiSeq, HiSeq 2000/2500, NextSeq 2000. Instrumentation NextSeq 500/550 Reference Material Indexing considerations for NextSeq 500/550 sample sheets A sample sheet is only required for offline analysis using bcl2fastq. If an invalid sample sheet in suspected, log files can help troubleshoot a failed analysis. Nov 5, 2024 路 The NextSeq 1000/2000 On-Prem Integration Package v1. A v2 Sample sheet template is available for download here. Follow the guidance in the Sample Sheet v2 Resource NextSeq 1000/2000 Settings to complete the sample sheet. Based on Illumina PhiX control library at supported cluster densities (between 129 and 165 k/mm² clusters passing filter). 0 enables run planning through the v2 sample sheet that is generated or imported. . For auto-launch compatible sample sheets, use BaseSpace Run Planner. Confirm the sample sheet version applicable to your sequencer to ensure the appropriate barcode sequences and sample sheets are supplied. These resources include software, training, compatible products, and the following documentation. csv) that stores the information needed to set up and analyze a sequencing experiment. csv) file that stores information required to set up The selected sample sheet must be in v2 format. Make sure any files referenced in the sample sheet Reference genomes and supporting JSON files for NextSeq 1000/2000 Control Software v1. The NextSeq 1000/2000 Sequencing System pages on the Illumina Support Site provide additional system resources. Used to identify the sample sheet as a v2 sample sheet. When the sample sheet is selected in the control software, it is copied to a pre-run folder on the instrument so the portable drive can be removed. The sample sheet is a comma-separated values (*. The NextSeq 1000/2000, NovaSeq 6000, and NovaSeq X/X Plus also support attaching a v2 sample sheet in manual mode to BSSH for auto launching BCL Convert instead. May 13, 2025 路 The BaseSpace Sequence Hub Run Planning tool is available, and is used to generate a valid sample sheet in v2 format for use on a supported sequencer for both ICA and Standalone DRAGEN Server analysis options. In the NextSeq 1000/2000 Control Software select the hamburger menu on the top-left corner. The integration also tracks both sequencing run and GenerateFASTQ analysis run events without a connection to BaseSpace Sequence Hub or ICA. 0. After editing, use a portable or mounted network drive to transfer the sample sheet to the NextSeq 1000 and NextSeq 2000 Sequencing Systems. Change in definition from prior release. The Generate bcl2fastq2 NextSeq SampleSheet automation uses the Template File Generator Innovations enabling productivity gains The NextSeq 1000 and NextSeq 2000 Systems leverage advances in optics, instrument design, and reagent chemistry to miniaturize the volume of the sequencing reaction while increasing output and reducing the cost per run. * The NextSeq 1000/2000, NovaSeq 6000, and NovaSeq X/X Plus also support attaching a v2 sample sheet in manual mode to BSSH for auto launching BCL Convert instead. Creating a corrected sample sheet Analysis of a NextSeq 1000/2000 run in BaseSpace Sequence Hub requires a correctly formatted v2 sample sheet. i5 index sequences should always be entered in the forward Sample sheets can be edited and FASTQ Generation analysis requeued for iSeq, MiniSeq (updated to Control Software 2 and Windows 10), MiSeq, HiSeq 1000/1500/2000/2500, NextSeq 500/550 (updated to Control Software 4 and Windows 10), and NovaSeq 6000 runs uploaded to BaseSpace Sequence Hub. Actual performance parameters may vary based on sample type, sample quality, and clusters passing filter. The NovaSeq X and 25B flow cell make ultra-high depth multiomics more accessible. For this option, all sample and index information is entered in Run Planning, and is included in the exported v2 sample sheet. Using BaseSpace Run Planning is recommended to generate a sample sheet for reanalysis to make sure that the required fields are correct. For generation and use of v2 sample sheets for BCL Convert, see the section on BaseSpace Run Planning below. The bcl2fastq2 sample sheet may be used with multiple instruments. csv) file that stores information required to set up, perform, and generate demultiplexed FASTQs from a sequencing run. 0). Sample Sheet Validation Failures In DRAGEN TruSight Oncology 500 Analysis Software, the analysis fails if a sample sheet is invalid. Samples are placed on the container to be loaded in the instrument. The sample sheet is a comma-delimited file (SampleSheet. The selected sample sheet must be in v2 format. 0) step. This field must always exist in the header section with a value of 2. Refer to ICA Auto-launch Sample Sheet Requirements for descriptions Apr 7, 2022 路 NOTE: It’s important to keep the Sample Sheet saved on the network drive or thumb drive as saving it locally on the instrument can cause errors. Get recommendations and resources so you can sequence with confidence. The generated sample sheet is intended to be used with the bcl2fastq conversion tool, provided by Illumina. Also see more on NextSeq 1000/2000 sample sheets in this blog from Illumina. IDT for Illumina TruSeq UD Indexes Sample Sheet Template for Local Run Manager A custom product file for use with IDT for Illumina TruSeq UD Indexes and the Local Run Manager software. Labs using both standard SBS and XLEAP-SBS kits consistently achieve data far above specifications for both yield and percentage of bases at or above Q30 (% ≥ Q30) on their NextSeq 1000 and NextSeq 2000 Systems. The reverse complement workflow is performed on the iSeq, MiniSeq, NextSeq 500, HiSeq 3000/4000/X. Deeper studies, more samples, more modalities. csv template. The default configuration provides the Generate bcl2fastq2 NextSeq SampleSheet automation. What is a Sample Sheet? A sample sheet is a comma-separated value (*. 7 and v2. qvcr1vm xuy9y mfe 3uobl 3qu q1phoss hjxq 719n i8b dwmx