Fiber-seq analysis pipeline
Fiber-seq is a long-read chromatin profiling method that uses a non-specific adenine methyltransferase to map protein occupancy and chromatin accessibility on individual DNA molecules, preserving linked sequence, CpG methylation, and haplotype information. It enables comprehensive genome-wide haplotype-resolved mapping of chromatin across entire diploid genomes, exposing how proteins co-occupy chromatin fibers and how variants affect local chromatin state.. To support reproducible and advanced analysis of Fiber-seq data, we have developed a suite of tools to QC and process Fiber-seq data.
GitHub site: https://fiberseq.github.io/
fibertools: https://github.com/fiberseq/fibertools-rs
FiberHMM: https://github.com/fiberseq/FiberHMM
FiberFold: https://github.com/altemoselab/fiberFold
Fiberseq-QC: https://github.com/fiberseq/fiberseq-qc
DAF-Seq Processing and QC Pipeline
DAF-seq is a long-read chromatin profiling method that uses deaminase marking to map protein occupancy and chromatin accessibility on individual DNA molecules, preserving linked sequence and haplotype information. It enables both targeted, as well as single-cell high-resolution views of regulatory architecture, including how proteins co-occupy chromatin fibers and how variants affect local chromatin state. To support reproducible analysis, we have generated a web resource that contains updated information on experimental design, targeted primer design, as well as a standardized QC pipeline (DAF-QC-SMK). The DAF-QC-SMK Snakemake pipeline performs standardized QC of DAF-seq data, including alignment, strand/deamination assessment, targeting metrics, deduplication, consensus generation, and summary reports.
GitHub site: https://fiberseq.github.io/The-Guide-for-DAF-seq/
Brotman Baty Institute Clinical Variant Database (BBI-CVD)
The BBI-CVD aims to serve as a hub connecting researchers studying rare disease genetics with clinicians applying precision genomics to care for patients with rare diseases. Specifically, the BBI-CVD contains a repository of genetic variants encountered during clinical testing at the University of Washington and Fred Hutch cancer center.
Our database contains Electronic health record (EHR)-linked germline genetic variants. Deidentified phenotypic information associated with each of the variants is available to researchers via our secure online data browser upon request.
To gain access to the data browser, please email our team at BBICVD@UW.edu, and we will follow up with the next steps.
Data hub: https://cvd.brotmanbaty.org/