Toil

Toil is a scalable, efficient, dynamic cross-platform pipeline management system written entirely in Python. Toil is being used by projects like the Treehouse childhood cancer initiative https://treehousegenomics.soe.ucsc.edu/ to create portable, scaleable and reproducible analyses. Toil was used to process over 20,000 RNA-seq samples in under …

Dockstore

Dockstore, developed by the Cancer Genome Collaboratory, is an open platform for sharing Docker-based tools described with the Common Workflow Language used by the GA4GH.

Xena

UCSC Xena

UCSC Xena is a bioinformatics tool to visualize functional genomics data from multiple sources simultaneously, including both public and private data. The Xena system consists of a set of federated data hubs and the Xena browser, which integrates across hubs, providing one location to analyze …

High Throughput Genomics Group

High Throughput Genomics Group

Genomics is in transition. The growth in data—driven by the need for vast sample sizes to gain statistical significance and the explosion of clinical sequencing—is far outpacing Moore’s law. Large projects like The Cancer Genome Atlas have generated petabyte scale datasets that very few groups …

Genome 10K

Genome 10K

The vertebrate evolutionary tree The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction in DNA sequencing suggests that this project will be …

Gencode screen shot http://www.gencodegenes.org/
View of a 56 Kbp region of human chromosome 17 where GENCODE annotates one non-coding and 5 protein coding genes. Two genes in the region display tissue-specific gene expression as evidenced by GTEx RNA-seq. The TCAP (titin cap protein) is highly expressed in muscle tissue, while PP1R1B (a therapeutic target for neurologic disorders) shows expression in brain basal ganglia but not muscle.

GENCODE

View of a 56 Kbp region of human chromosome 17 where GENCODE annotates one non-coding and 5 protein coding genes. Two genes in the region display tissue-specific gene expression as evidenced by GTEx RNA-seq. The TCAP (titin cap protein) is highly expressed in muscle tissue, …

Computational Nanopore Genomics

Nanopore technology is emerging as one of the leading contenders for next generation sequencing. The concept of nanopore sequencing was envisioned in the early 1990s by David Deamer (UC Santa Cruz) and Daniel Branton (Harvard). The recent commercialization of the technology, particularly the Oxford Nanopore’s …

BRCA Exchange pink ribbon logo

BRCA Exchange

  We are developing the BRCA Exchange, a comprehensive, global data repository to catalogue variation within the BRCA genes and to collect individual-level evidence for their classification. The scientific and medical communities have a tremendous and urgent need for a comprehensive data store of variants …

Global Alliance for Genomics and Health Integration Group

Global Alliance for Genomics and Health Integration Group

The Global Alliance for Genomics and Health (GA4GH) is an international effort to promote, foster and standardize secure, ethical, privacy preserving sharing of genomic information for the betterment of global health outcomes. It has many, many organizations involved, all recognizing the importance of its mission, …

genome graph for the Leukocyte Receptor Complex
A genome graph for the Leukocyte Receptor Complex built from 30 underlying human haplotypes

Human Genome Variation Map

A genome graph for the Leukocyte Receptor Complex built from 30 underlying human haplotypes Since UC Santa Cruz researchers posted the first draft of the human genome on the Internet in 2000, the current model of human genetics in the genome era has not changed: …