CCR Collaborative Bioinformatics Resource
Table of Contents
- 🎉 Recent Releases (last 3 months)
- TOP contributors
- About Us
- Our model
- Pipelines
- Tools
ccbrpipelinermodule release history on BIOWULF- 📦 Full Release History
- Days since last activity
- Citation
🎉 Recent Releases (last 3 months)
| Repo Name | Release Name | Release Date | Open Issues |
|---|---|---|---|
| SINCLAIR | v0.4.0 | 2026-05-13 | 52 |
| MOSuite | v0.3.1 | 2026-05-07 | 32 |
| CARLISLE | v2.7.6 | 2026-05-06 | 20 |
| actions | v0.6.2 | 2026-04-23 | 13 |
| CHAMPAGNE | v0.6.0 | 2026-04-17 | 54 |
| RENEE | v2.7.5 | 2026-04-06 | 23 |
| Tools | v0.5.2 | 2026-03-24 | 9 |
TOP contributors
| User | Total Commits | Commits in Last Month | Commits in Last 6 Months |
|---|---|---|---|
| kelly-sovacool | 7040 | 172 | 1186 |
| kopardev | 2986 | 58 | 187 |
| finneyr | 331 | 0 | 0 |
| escauley | 243 | 15 | 73 |
| kvaldez | 223 | 0 | 0 |
| wong-nw | 209 | 7 | 50 |
| samarth8392 | 190 | 6 | 33 |
| maggiecam | 53 | 0 | 0 |
| pajailwala | 52 | 5 | 29 |
| bianjh-cloud | 43 | 10 | 37 |
About Us
- 👋 Hi, we’re the @CCBR, a group of bioinformatics analysts and engineers
- 📖 We build flexible, reproducible, workflows for next-generation sequencing data
- 💡 We collaborate with CCR PIs
- 📫 You can reach us at ccbr_pipeliner@mail.nih.gov
- 🏁 Check out our release history
- 🔗 Our Zenodo community
🆘 Need Help?
📧 Email us at ccbr_pipeliner@mail.nih.gov — we’re always happy to help!
🗓️ Weekly Office Hours — Thursdays, 3–5 PM - 📍 In-person: Bethesda Campus, Building 37, Room 3041 - 💻 Virtual: Join via Microsoft Teams
Our model
Got data? We’ve got you covered! 🎉 The CCR Collaborative Bioinformatics Resource (CCBR) is your one-stop shop for bioinformatics support at the National Cancer Institute’s Center for Cancer Research (CCR). We’re a powerhouse team of bioinformatics experts drawn from across NCI — including the CCR Office of Science and Technology Resources (OSTR), the Frederick National Laboratory for Cancer Research (FNLCR), and the Center for Biomedical Informatics and Information Technology (CBIIT) — all united by one mission: turning your raw data into discovery.
Whether you need help with experimental design, data analysis, pipeline development, or training, we make it easy to get started. Just submit a request and we’ll take it from there — with personalized consultations (in-person or virtual!) tailored to your project’s needs. No bioinformatics background required on your end; that’s literally what we’re here for. 🙌
We operate through two complementary teams that together keep CCR researchers moving forward:
-
🏢 The Core Team — Our centralized squad available to any CCR researcher. From bulk RNA-seq to whole-genome analysis, we bring broad expertise and dedicated bandwidth to help you tackle the big questions.
-
🔬 The Embedded Team — Bioinformaticians embedded directly within specific labs and research groups, providing day-to-day, hands-on support with deep familiarity of your ongoing projects. Think of them as your in-house bioinformatics colleagues!
💡 Ready to get started? Visit CCBR’s official website or reach out directly — we’d love to work with you!
Pipelines
CCBR offers end-to-end analysis pipelines for NGS data analysis.
Here is a list of our prominent pipelines and their release schedule on BIOWULF:
| Data Type | Pipeline Name | Description | CLI* available since |
|---|---|---|---|
| RNASeq1 | RENEE |
Comprehensive RNA-seq workflow that combines contamination screening, adapter trimming, two-pass STAR alignment, and RSEM quantification. It generates gene and isoform count matrices, fusion calls, and MultiQC-style quality summaries for cohort-level review. | July 3rd 2023 |
| WESSeq2 | XAVIER |
Whole-exome sequencing pipeline aligned to Broad-style best practices using a reproducible Snakemake execution model. It accepts FASTQ or BAM inputs and supports germline and somatic variant calling, CNV inference, and downstream annotation. | July 21st 2023 |
| ATACSeq3 | ASPEN |
ATAC-seq analysis workflow for preliminary QC, peak calling, and differential chromatin accessibility testing. It is configured for Biowulf usage and provides standardized outputs for regulatory genomics interpretation. | November 30th 2023 |
| ChIPSeq4 | CHAMPAGNE |
ChIP-seq analysis pipeline with support for configurable reference genomes and optional spike-in genome handling. It produces reproducible peak-centric outputs from aligned sequencing data and can be run through CCBR module-based workflows. | October 15th 2023 |
| CRISPRSeq5 | CRISPIN |
CRISPR screen sequencing workflow designed for reproducible run setup and execution on Biowulf. It processes screening libraries into analysis-ready outputs suitable for guide-level and gene-level interpretation. | September 2023 |
| CUT&RunSeq6 | CARLISLE |
CUT&RUN pipeline that performs peak calling with MACS2, SEACR, and GoPeaks using spike-in-normalized FASTQ inputs. It is built in Snakemake and tuned for reproducible chromatin profiling on Biowulf. | October 31st 2023 |
| EV-Seq10 | ESCAPE |
Extracellular vesicle RNA-seq workflow for EV-derived libraries from raw reads through analysis-ready quantification outputs. It emphasizes consistent QC and standardized processing for comparative EV transcriptomics. | March 26th 2024 |
| circRNASeq7 | CHARLIE |
circRNA pipeline for detection, annotation, and quantification of host and viral circular RNAs. It orchestrates multiple circRNA callers in parallel, including CIRCExplorer2 and CIRI2-based paths, to support robust cross-method discovery. | September 16th 2024 |
| scRNASeq8 | SINCLAIR |
Single-cell analysis resource supporting multiple next-generation modalities in a reproducible Nextflow framework. It starts from FASTQ or h5-aligned inputs, performs per-sample QC, and generates per-contrast integration reports. | February 28th 2025 |
| WGSSeq9 | LOGAN |
Whole-genome sequencing pipeline based on Broad-aligned processing patterns and Nextflow orchestration. It calls and annotates germline and somatic variants, CNVs, and SVs with reproducible containerized execution. | May 31st 2025 |
| spatialSeq11 | SPENCER |
Spatial sequencing workflow for processing location-aware transcriptomic measurements across tissue regions. It is designed to produce structured outputs for downstream spatial feature analysis, integration, and visualization. | TBD |
* CLI = Command Line Interface
ℹ️ GUI (Graphical User Interface) development has been suspended for the time being but may resume in the future.
1 RENEE=Rna sEquencing aNalysis pipElinE.
2 XAVIER=eXome Analysis and Variant explorER.
3 ASPEN=Atac Seq PipEliNe.
4 CHAMPAGNE=CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline.
5 CRISPIN=CRISPr screen sequencing analysis pipelINe.
6 CARLISLE=Cut And Run anaLysIS pipeLinE.
7 CHARLIE=Circrnas in Host And viRuses anaLysis pIpEline.
8 SINCLAIR=SINgle CelL AnalysIs Resource.
9 LOGAN=whoLe genOme-sequencinG Analysis pipeliNe.
10 ESCAPE=Extracellular veSiCles rnAseq PipelinE.
11 SPENCER=SPatial sequENCing Resource.
For any other datatype or pipeline, please email us 📬 directly to get the conversation started!
Tools
In addition to end-to-end analysis pipelines, the CCBR dev team also builds tools for data management, metadata management, and HPC utilities:
| Tool | Description |
|---|---|
| spacesavers2 | 🚀 Crawls HPC folders to identify duplicate files and report how much disk space can be reclaimed — essential for keeping Biowulf storage lean |
| parkit | 🅿️ Archives completed project data (folders or tarballs) from Biowulf/Helix to the HPC-DME CCBR_Archive vault for long-term storage |
| permfix | 🔐 Fixes folder and file permissions for Biowulf users — handy when shared project directories get locked down |
ccbrpipeliner module release history on BIOWULF
module load ccbrpipeliner loads the default release of ccbrpipeliner
on BIOWULF. Each release comprises a unique combination of pipeline
versions bundled together.
⚠️ Older releases remain available on BIOWULF but may not function as originally intended — changes to HPC modules, dependencies, or system software over time can affect behavior. We recommend using the current default release whenever possible.
| Release | Tool versions | Released on | Decommissioned on |
|---|---|---|---|
| 1 | RENEE v2.1 @# | July, 10th 2023 | July, 14th 2023 |
| 2 | RENEE v2.2 @# | July, 14th 2023 | September, 5th 2023 |
| 3 | RENEE v2.2 @#, XAVIER v2.0 @ |
July, 21st 2023 | - |
| 4 | RENEE v2.5 @#, XAVIER v3.0 @# |
September, 5th 2023 | - |
| 5 | RENEE v2.5 @#, XAVIER v3.0 @#, CARLISLE v2.4 @, CHAMPAGNE v0.2 @, CRUISE v0.1 @, spacesavers2 v0.10 @, permfix v0.6 @ |
October, 27th 2023 | - |
| 6 | RENEE v2.5 @#, XAVIER v3.0 @#, CARLISLE v2.4 @, CHAMPAGNE v0.3 @, CRUISE v0.1 @, ASPEN v1.0 @, spacesavers2 v0.12 @, permfix v0.6 @ |
February, 29th 2024 | - |
| 7 | RENEE v2.6 @#, XAVIER v3.1 @#, CARLISLE v2.6 @, CHAMPAGNE v0.4 @, CHARLIE v0.11 @, CRISPIN v1.0 @ (previously CRUISE), ASPEN v1.0 @, spacesavers2 v0.14 @, permfix v0.6 @, ccbr_tools v0.1 @ |
Jan, 10th 2025 | - |
| 8* | RENEE v2.7 @#, XAVIER v3.2 @#, CARLISLE v2.7 @, CHAMPAGNE v0.5 @, CHARLIE v0.12 @, CRISPIN v1.2 @, ASPEN v1.1 @, ESCAPE v1.2 @, LOGAN v0.3 @, SINCLAIR v0.3 @, spacesavers2 v0.14 @, permfix v0.6 @, ccbr_tools v0.4 @ |
Jul, 18th 2025 | - |
* = Current DEFAULT version on BIOWULF
@ = CLI available
# = GUI available
module load ccbrpipelineris also available on HELIX. It only loads the tools and not the pipelines as HELIX does not have a job scheduler
📦 Full Release History
| Repo Name | Release Name | Release Date | Open Issues |
|---|---|---|---|
| SINCLAIR | v0.4.0 | 2026-05-13 | 52 |
| MOSuite | v0.3.1 | 2026-05-07 | 32 |
| CARLISLE | v2.7.6 | 2026-05-06 | 20 |
| actions | v0.6.2 | 2026-04-23 | 13 |
| CHAMPAGNE | v0.6.0 | 2026-04-17 | 54 |
| RENEE | v2.7.5 | 2026-04-06 | 23 |
| Tools | v0.5.2 | 2026-03-24 | 9 |
| HowTos | v1.1.0 | 2026-02-23 | 16 |
| parkit | v3.0.1 | 2026-02-19 | 0 |
| LOGAN | v0.3.3 | 2026-02-12 | 21 |
| XAVIER | v3.2.2 | 2026-01-29 | 10 |
| ASPEN | v1.1.2 | 2025-07-17 | 18 |
| spacesavers2 | v0.14.1 | 2025-07-15 | 7 |
| CCBR_tobias | v0.3.1 | 2025-06-23 | 3 |
| TRANQUIL | v0.3.0 | 2025-06-16 | 3 |
| CRISPIN | v1.2.1 | 2025-05-28 | 22 |
| CHARLIE | v0.12.0 | 2025-05-20 | 14 |
| Dockers2 | v0.1.2 | 2024-12-02 | 6 |
| METRO | v2.1 | 2024-03-28 | 2 |
| CCBR-1144 | v1.0.0 | 2024-03-04 | 0 |
| ccbr1271_ERVpipeline | v1.0.3 | 2024-02-21 | 1 |
| nf-modules | v0.1.0 | 2023-11-29 | 16 |
| CRISPRAnnotation | v1.0 | 2023-10-19 | 0 |
| SharanLab | v1.0.0 | 2023-07-18 | 0 |
| Pipeliner | v4.0.7 | 2023-05-09 | 24 |
| MAPLE | v1.0.1 | 2023-02-27 | 0 |
| DTB_ExomeSeq | v1.0 | 2022-06-22 | 0 |
| ASCENT | v0.1.1 | 2022-01-04 | 2 |
| CCBR_circRNA_AmpliconSeq | v0.1.1 | 2021-03-24 | 0 |
| rNA | v1.0.0 | 2021-01-21 | 0 |
| l2p | v0.0.3 | 2020-07-13 | 0 |
| MAAPster | v2.0.0 | 2020-04-27 | 0 |
Days since last activity
Citation
Most of our end-to-end pipelines which have been used in published research work have been made available to the entire bioinformatics community via a Zenodo DOI. Please feel free to visit our Zenodo community page. And if you use our pipelines, don’t forget to cite us!