UC Santa Cruz Genomics Institute - Computational Genomics Lab (@BD2KGenomics)
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BD2KGenomics

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Top repositories

1

toil-rnaseq

UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline
Python
38
star
2

toil-scripts

Toil workflows for common genomic pipelines
Python
32
star
3

protect

Python
28
star
4

cgcloud

Image and VM management for Jenkins, Spark and Mesos clusters in EC2
Python
22
star
5

cgl-docker-lib

Python
21
star
6

conductor

Efficient, distributed downloads of large files from S3 to HDFS using Spark.
Scala
17
star
7

s3am

A fast, parallel, streaming multipart uploader for S3
Python
13
star
8

hgvm-graph-bakeoff-evaluations

All code for reproducing reference graph bakeoff results
Python
9
star
9

bioapi-examples

Code examples for working with web based bioinformatics APIs
Jupyter Notebook
9
star
10

brca-website-deprecated

This repo is deprecated! Please use https://github.com/BD2KGenomics/brca-exchange
JavaScript
6
star
11

23andMe-brca-exchange

Get expert, curated information about your 23andMe results in the BRCA1 and 2 regions
Python
5
star
12

toil-lib

A common library for functions and tools used in toil-based pipelines
Python
4
star
13

bd2k-python-lib

The BD2K Python module kitchen sink
Python
4
star
14

brca-pipeline

This repo is deprecated! Please use https://github.com/BD2KGenomics/brca-exchange
Python
4
star
15

dcc-metadata-indexer

Scripts and schemas for JSON documents used with the DCC storage system and for building Elasticsearch indexes
Python
4
star
16

core-operations

test repo for core operation
Python
3
star
17

hgvm-builder

Tool to build a (Human) Genome Variation Map from a set of data sources
Python
3
star
18

adam-contest-eval

Run ADAM variant calling against the 1000genomes.org dataset
Shell
3
star
19

vcf-to-ga

Generates GA4GH messages from VCF data
Python
3
star
20

dockstore_tool_adtex

R
2
star
21

dcc-redwood-client

Shell
2
star
22

dockstore_workflow_fusion

Runs STARFusion and arriba
Common Workflow Language
2
star
23

10k-exomes

Python
2
star
24

toil-rnaseq-sc

Toil-based RNA-seq pipeline for processing single-cell data
Python
2
star
25

dockstore_workflow_snps

Workflow for variant callers MuSE, MuTect, SomaticSniper, and Pindel
Common Workflow Language
2
star
26

dockstore_tool_varscan_cnv

Varscan copynumber variation caller workflow
Shell
2
star
27

toil-topmed

The repository for the Toil TOPMed alignment best practice workflow.
Python
2
star
28

dcc-ops

The UCSC Genomics Institute's Computational Genomics Platform (CGP). This repo contains the Docker compose-based deployment process.
Shell
2
star
29

hgvm

Python
2
star
30

toil-workflows

Modern Toil Workflows
Common Workflow Language
2
star
31

ga4gh-gemini

Providing a GA4GH Interface to Gemini Variant Data
Protocol Buffer
1
star
32

hgvm-aligner-bakeoff-compliance

Tools and specifications for aligner behavior in the graph aligner bake-off
1
star
33

ga4gh-integration-deprecated

Tracking for ga4gh-integration projects
1
star
34

false-tandem-dup-finder

Scripts to find false tandem dups around scaffold gaps
Python
1
star
35

dockstore_workflow_cnv

Runs ADTEx and Varscan copynumber on input exome bam files
1
star
36

dcc-feature-requests

Add feature requests for the UCSC GI Computational Platform here
1
star
37

cgl-hr

A public wiki for open projects in the CGL lab
1
star
38

driver-projects

1
star
39

DREAMChallenges

a place to track work on the GA4GH Dream Challenges
1
star
40

platform-administration

Issues representing platform epics, user stories, tasks, etc. that are not specific to an existing component repository.
1
star
41

fhir-ga4gh-integration

Improve integration of FHIR Genomics and GA4GH
1
star
42

dcc-spinnaker-client

The submission system client that uploads data/metadata to Redwood and indicates to the Spinnaker web service that a submission bundle is ready for validation.
Python
1
star
43

dcc-metadata-schemas

Repository for our JSON schema's used to describe our common metadata model.
1
star
44

dcc-redwood-compose

Shell
1
star
45

dockstore_tool_arriba

Implementation of structural variant finding algorithm arriba by Sebastian Uhrig
Shell
1
star
46

dcc-spinnaker

The server web service and UI for interacting with the Spinnaker validation system.
Python
1
star
47

parasol-binaries

A stop-gap for hosting parasol binaries. If in doubt, ignore this.
1
star
48

dcc-auth-proxy

Proxy in front of dcc services ensuring the right people are passed through with the right privileges
JavaScript
1
star
49

dcc-dockstore-tool-runner

A Dockstore tool designed to perform file downloads from Redwood, run another Dockstore tool, and then upload to Redwood.
Python
1
star
50

dcc-action-service

A place for our business logic written in Luigi that triggers workflow launches.
Python
1
star
51

dockstore-tool-gene-by-cell-creator

creates a gene by cell matrix from multiple slices
Python
1
star