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Seeker Bioinformatics Solutions

The comprehensive Seeker Bioinformatics Solutions include the Seeker Primary Analysis Pipeline and the Secondary Data Analysis Workflow.

Ways to run Seeker Bioinformatics Solutions

Local: via installation on local workstations or clusters. Access installation and usage instructions by completing the form below.
Cloud: via cloud analysis on the Takara Bio Spatial Bioinformatics Portal.

The Seeker Primary Analysis Pipeline processes FASTQ files generated from Seeker sequencing libraries for high resolution spatial transcriptomic analysis in a single, efficient package. The pipeline reconstructs a spatial map of gene expression as well as provides quality control and preliminary cluster and spatial variable gene analyses in a simple .html report for initial data interpretation of the Seeker experiment.

The Seekker Primary Analysis Pipeline requires:

Paired end FASTQ files (without adapter trimming) generated from sequenced libraries
Tile bead barcode file for the Seeker tile used
Sample sheet with reference genome for the species surveyed associating sample metadata with aforementioned inputs

The Secondary Data Analysis workflow is a summary of popular tools developed by the scientific community to process the html output of the Trekker Primary Analysis Pipeline and Seeker Primary Analysis Pipeline. This workflow provides guidelines specifically designed for Trekker and Seeker data.

Cat. #	Product	Size	Price	Quantity
650014	Cogent™ NGS Immune Viewer v1.0	Each	Inquire for Quotation	*
Notice to purchaser Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval.
650005.V3.2	Cogent™ NGS Analysis Pipeline	Each	Inquire for Quotation	*
Notice to purchaser Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval.

*You must be logged in to a Purchasing Account in order to purchase these products online, since the purchase of these products may be restricted depending on your account type. Researchers at not-for-profit accounts receive a limited use license with their purchase of the product. Researchers at for-profit accounts must obtain a license prior to purchase. For details please contact licensing@takarabio.com.

More Information

Supported operating systems

Linux platforms with ≥ 256 GB RAM and 32 cores.

IMPORTANT: The pipeline does NOT support MacOS or Windows operating systems.

Additional third-party software dependencies*

The Seeker bioinformatics pipeline is written in Nextflow. Its dependencies can be executed through either Singularity (Apptainer) or Docker.

Not included with the software; must be downloaded and installed separately.

Seeker Primary Analysis Pipeline version history

Version number	Release date	Notes
v3.1.0	2025-08	New features STAR Alignment and FORMATCLEANUP: Now automatically retry with progressively increased memory on failure. Bug fixes FORMATCLEANUP: Fixed edge case handling for last count matrix chunk containing only one bead barcode. GENEREPORT: Dynamically adjusts color palette size to support datasets with many clusters. ANALYSIS: Resolved issue with reticulate failing to locate the anndata module by enforcing use of the Seeker conda environment. STAR Alignment: Updated container from star:2.6.1d--0 to star:2.6.1d--h9ee0642_1 for compatibility with newer Docker/Singularity versions. FEATURECOUNT: Updated Subread container from 2.0.1 to 2.0.8 to fix segmentation faults on large genomes. Workflow simplification Bundled Seeker, STAR, Samtools, and Subread Singularity and Docker containers directly into the codebase. This removes the need to pull containers separately or configure singularity paths and cache directories.
v3.0.0	2024-06	Impact Algorithmic improvements, chunk size optimization, and reorganization of steps have been implemented, leading to lower memory requirements (256 GB for up to 3B reads) and decreased execution time (32-63% compared with v2.0.0). Minimal output change as compared to v2.0.0. Now compatible with Sequera Nextflow Tower platform. Bugs fixed for commonly encountered user issues, due to different storage setups, varying data sizes,and varying data quality. This results in a higher percentage of successful executions without user intervention and improved user experience. 6 new prebuilt references are available for download. Optional cleanup of intermediate files, leading to a smaller output footprint. Optimization and efficiency Merged processes GENBARCODES and CALCULATETOPBB into a single process CALCULATETOPBB_COMBINED. Removed process MERGE_READ1_READ2_DB. Removed process FORMATCONVERT. Renamed process UMITOOLSCOUNTSX as UMITOOLSCOUNTSG. Process CALCULATETOPBB_COMBINED was optimized for efficient memory and CPU utilization. Process FORMATCLEANUP was optimized for efficient memory utilization, through chunk size reduction from 165,000 to 100,000. Optimized resource allocation strategy for faster and less expensive distributed cloud computing. Optimized default resource allocation and chunk sizes for adaptability to a wider range of dataset sizes (up to 3 billion reads). Bug fixes Assorted container mounts were replaced with dedicated Nextflow channels, eliminating the need for explicitly declared volumes. -STAR alignment genome file inaccessible bug fixed -samplesheet.csv inaccessible bug fixed GEN_GENE_BARCODE_UMI_DB: pyarrow.lib.ArrowNotImplementedError:Unsupported cast from string to null using function cast_null) bug fixed. FORMATCONVERT: RuntimeError: cannot cache function 'sparse_mean_var_minor_axis': no locator available for file bug fixed. FORMATCLEANUP: ‘out_of_memory’ bug fixed. New Features Full Nextflow Tower compatibility. --clean_work option added: removal of intermediate and temporary work files after successful pipeline executions. Execution command and input changes --igenomes_base: no longer required for execution using custom genome reference. samplesheet.csv: for execution using custom genome reference, only 2 additional columns (star_index, gtf) are required. Output changes ${sample}_anndata.h5ad: Additional information is added to this output, including dimensional reduction outcomes, cluster assignments, and quality control metrics. They are obtained via the FORMATCLENUP and ANALYSIS processes and visualized in the html report. New prebuilt genome references Drosophila melanogaster Macaca mulatta Callithrix jacchus Poecilia reticulata Sorghum bicolor Xenopus laevis

Version number

Release date

Notes

v3.1.0

2025-08

New features

STAR Alignment and FORMATCLEANUP: Now automatically retry with progressively increased memory on failure.

Bug fixes

FORMATCLEANUP: Fixed edge case handling for last count matrix chunk containing only one bead barcode.
GENEREPORT: Dynamically adjusts color palette size to support datasets with many clusters.
ANALYSIS: Resolved issue with reticulate failing to locate the anndata module by enforcing use of the Seeker conda environment.
STAR Alignment: Updated container from star:2.6.1d--0 to star:2.6.1d--h9ee0642_1 for compatibility with newer Docker/Singularity versions.

FEATURECOUNT: Updated Subread container from 2.0.1 to 2.0.8 to fix segmentation faults on large genomes.

Workflow simplification

Bundled Seeker, STAR, Samtools, and Subread Singularity and Docker containers directly into the codebase. This removes the need to pull containers separately or configure singularity paths and cache directories.

v3.0.0

2024-06

Impact

Algorithmic improvements, chunk size optimization, and reorganization of steps have been implemented, leading to lower memory requirements (256 GB for up to 3B reads) and decreased execution time (32-63% compared with v2.0.0).
Minimal output change as compared to v2.0.0.
Now compatible with Sequera Nextflow Tower platform.
Bugs fixed for commonly encountered user issues, due to different storage setups, varying data sizes,and varying data quality. This results in a higher percentage of successful executions without user intervention and improved user experience.
6 new prebuilt references are available for download.
Optional cleanup of intermediate files, leading to a smaller output footprint.

Optimization and efficiency

Merged processes GENBARCODES and CALCULATETOPBB into a single process
CALCULATETOPBB_COMBINED.
Removed process MERGE_READ1_READ2_DB.
Removed process FORMATCONVERT.
Renamed process UMITOOLSCOUNTSX as UMITOOLSCOUNTSG.
Process CALCULATETOPBB_COMBINED was optimized for efficient memory and CPU utilization.
Process FORMATCLEANUP was optimized for efficient memory utilization, through chunk size reduction from 165,000 to 100,000.
Optimized resource allocation strategy for faster and less expensive distributed cloud computing.
Optimized default resource allocation and chunk sizes for adaptability to a wider range of dataset sizes (up to 3 billion reads).

Bug fixes

Assorted container mounts were replaced with dedicated Nextflow channels, eliminating the need for explicitly declared volumes.
-STAR alignment genome file inaccessible bug fixed
-samplesheet.csv inaccessible bug fixed
GEN_GENE_BARCODE_UMI_DB: pyarrow.lib.ArrowNotImplementedError:Unsupported cast from string to null using function cast_null) bug fixed.
FORMATCONVERT: RuntimeError: cannot cache function 'sparse_mean_var_minor_axis': no locator available for file bug fixed.
FORMATCLEANUP: ‘out_of_memory’ bug fixed.

New Features

Full Nextflow Tower compatibility.
--clean_work option added: removal of intermediate and temporary work files after successful pipeline executions.

Execution command and input changes

--igenomes_base: no longer required for execution using custom genome reference.
samplesheet.csv: for execution using custom genome reference, only 2 additional columns (star_index, gtf) are required.

Output changes

${sample}_anndata.h5ad: Additional information is added to this output, including dimensional reduction outcomes, cluster assignments, and quality control metrics. They are obtained via the FORMATCLENUP and ANALYSIS processes and visualized in the html report.

New prebuilt genome references

Drosophila melanogaster
Macaca mulatta
Callithrix jacchus
Poecilia reticulata
Sorghum bicolor
Xenopus laevis

Download the software

If you are interested in using the Seeker Bioinformatics Solutions, please review the End User License Agreement (EULA) before populating the required fields of the form.

After checking the box to indicate acceptance of the EULA and submitting the completed form, your browser will be directed to a page where you can download the software.

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