Most of our work has resulted in scholarly publications. On this page you can review our publications to get an idea about our work.
github.com/broadinstitute/warp/PairedTag
July, 2026 • Software
broadinstitute
WDL Analysis Research Pipelines
The WDL Analysis Research Pipelines (WARP) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data Sciences…
WDL Analysis Research Pipelines
The WDL Analysis Research Pipelines (WARP) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data Sciences Platform and collaborators.
WARP provides robust, standardized data analysis for the Broad Institute Genomics Platform and large consortia like the Human Cell Atlas and the BRAIN Initiative. WARP pipelines are rigorously scientifically validated, high scale, reproducible and open source, released under the BSD 3-Clause license.
Pipeline releases
All pipeline releases are listed on the WARP releases page. To discover and search releases, use the WARP command-line tool Wreleaser.
WARP Dockers and custom tools in warp-tools repository
All Dockers and custom tools used for WARP's WDL Workflows are maintained in a separate repository, warp-tools.
WARP documentation
Read more about our pipelines and repository on the WARP documentation site.
To contribute to WARP, please read the contribution guidelines.
The optimus 3' pipeline processes 10x genomics sequencing data based on the v2 chemistry. It corrects cell barcodes and UMIs, aligns reads, marks duplicates, and returns data as alignments in BAM form…
The optimus 3' pipeline processes 10x genomics sequencing data based on the v2 chemistry. It corrects cell barcodes and UMIs, aligns reads, marks duplicates, and returns data as alignments in BAM format and as counts in sparse matrix exchange format.
Warp Analysis Research Pipelines
The Warp Analysis Research Pipelines (WARP) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data Scienc…
Warp Analysis Research Pipelines
The Warp Analysis Research Pipelines (WARP) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data Sciences Platform and collaborators.
WARP provides robust, standardized data analysis for the Broad Institute Genomics Platform and large consortia like the Human Cell Atlas and the BRAIN Initiative. WARP pipelines are rigorously scientifically validated, high scale, reproducible and open source, released under the BSD 3-Clause license.
Pipeline releases
All pipeline releases are listed on the WARP releases page. To discover and search releases, use the WARP command-line tool Wreleaser.
WARP Dockers and custom tools in warp-tools repository
All Dockers and custom tools used for WARP's WDL Workflows are maintained in a separate repository, warp-tools.
WARP documentation
Read more about our pipelines and repository on the WARP documentation site.
To contribute to WARP, please read the contribution guidelines.
Citing WARP
When citing WARP, please use the following:
Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konwar, K.; Mathews, K.; Palis, K.; Petrillo, N.; Van der Auwera, G.; Wang, C.; Way, J.; Pipelines, W. WDL Analysis Research Pipelines: Cloud-Optimized Workflows for Biological Data Processing and Reproducible Analysis. Preprints 2024, 2024012131. https://doi.org/10.20944/preprints202401.2131.v1
This workflow builds a combined mtDNA MatrixTable from per-sample VCFs, imputes hom-ref coverage from a coverage DB, and outputs annotated (full and filtered) callsets.
Warp Analysis Research Pipelines
The Warp Analysis Research Pipelines (WARP) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data Scienc…
Warp Analysis Research Pipelines
The Warp Analysis Research Pipelines (WARP) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data Sciences Platform and collaborators.
WARP provides robust, standardized data analysis for the Broad Institute Genomics Platform and large consortia like the Human Cell Atlas and the BRAIN Initiative. WARP pipelines are rigorously scientifically validated, high scale, reproducible and open source, released under the BSD 3-Clause license.
Pipeline releases
All pipeline releases are listed on the WARP releases page. To discover and search releases, use the WARP command-line tool Wreleaser.
WARP Dockers and custom tools in warp-tools repository
All Dockers and custom tools used for WARP's WDL Workflows are maintained in a separate repository, warp-tools.
WARP documentation
Read more about our pipelines and repository on the WARP documentation site.
To contribute to WARP, please read the contribution guidelines.
Citing WARP
When citing WARP, please use the following:
Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konwar, K.; Mathews, K.; Palis, K.; Petrillo, N.; Van der Auwera, G.; Wang, C.; Way, J.; Pipelines, W. WDL Analysis Research Pipelines: Cloud-Optimized Workflows for Biological Data Processing and Reproducible Analysis. Preprints 2024, 2024012131. https://doi.org/10.20944/preprints202401.2131.v1
Warp Analysis Research Pipelines
The Warp Analysis Research Pipelines (WARP) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data Scienc…
Warp Analysis Research Pipelines
The Warp Analysis Research Pipelines (WARP) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data Sciences Platform and collaborators.
WARP provides robust, standardized data analysis for the Broad Institute Genomics Platform and large consortia like the Human Cell Atlas and the BRAIN Initiative. WARP pipelines are rigorously scientifically validated, high scale, reproducible and open source, released under the BSD 3-Clause license.
Pipeline releases
All pipeline releases are listed on the WARP releases page. To discover and search releases, use the WARP command-line tool Wreleaser.
WARP Dockers and custom tools in warp-tools repository
All Dockers and custom tools used for WARP's WDL Workflows are maintained in a separate repository, warp-tools.
WARP documentation
Read more about our pipelines and repository on the WARP documentation site.
To contribute to WARP, please read the contribution guidelines.
Citing WARP
When citing WARP, please use the following:
Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konwar, K.; Mathews, K.; Palis, K.; Petrillo, N.; Van der Auwera, G.; Wang, C.; Way, J.; Pipelines, W. WDL Analysis Research Pipelines: Cloud-Optimized Workflows for Biological Data Processing and Reproducible Analysis. Preprints 2024, 2024012131. https://doi.org/10.20944/preprints202401.2131.v1
Warp Analysis Research Pipelines
The Warp Analysis Research Pipelines (WARP) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data Scienc…
Warp Analysis Research Pipelines
The Warp Analysis Research Pipelines (WARP) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data Sciences Platform and collaborators.
WARP provides robust, standardized data analysis for the Broad Institute Genomics Platform and large consortia like the Human Cell Atlas and the BRAIN Initiative. WARP pipelines are rigorously scientifically validated, high scale, reproducible and open source, released under the BSD 3-Clause license.
Pipeline releases
All pipeline releases are listed on the WARP releases page. To discover and search releases, use the WARP command-line tool Wreleaser.
WARP Dockers and custom tools in warp-tools repository
All Dockers and custom tools used for WARP's WDL Workflows are maintained in a separate repository, warp-tools.
WARP documentation
Read more about our pipelines and repository on the WARP documentation site.
To contribute to WARP, please read the contribution guidelines.
Citing WARP
When citing WARP, please use the following:
Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konwar, K.; Mathews, K.; Palis, K.; Petrillo, N.; Van der Auwera, G.; Wang, C.; Way, J.; Pipelines, W. WDL Analysis Research Pipelines: Cloud-Optimized Workflows for Biological Data Processing and Reproducible Analysis. Preprints 2024, 2024012131. https://doi.org/10.20944/preprints202401.2131.v1
Reproducibility code for repeated-decision course-withdrawal auditing in OULAD
August, 2026 • Software
Wu, Suhan, Luo, Min
This software archive reproduces the numerical analyses, five result tables, and five data-generated figures for a repeated-decision audit of course-withdrawal early-warning models in the Open Univers…
This software archive reproduces the numerical analyses, five result tables, and five data-generated figures for a repeated-decision audit of course-withdrawal early-warning models in the Open University Learning Analytics Dataset (OULAD). The workflow reconstructs landmark-specific risk sets, performs development-only model selection and calibration with temporal testing, evaluates capacity-constrained alert lists and their stability, implements matched-cohort and dependence sensitivities, conducts a retrospectively protocolized subgroup audit, and generates trajectory-consistent perturbations from event-level learning-platform records. A single entry point verifies source-data hashes, runs the test suite and complete analysis, regenerates publication assets, and checks principal results against compact reference fixtures. The conceptual framework diagram and manuscript text are outside this archive.
There is an increasing interest in upgrading the EModel, a parametric tool for speech quality estimation, to the wideband and super-wideband contexts. The
Contemporary models of Unmanned Aerial Vehicles (UAVs) are largely developed using simulators. In a typical scheme, a flight simulator is dovetailed with a
Undertaking engineering research can be compounding for beginning graduate students and thwarting even for seasoned researchers. With a wealth of academic
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