No description, website, or topics provided.
JavaScript Python HTML Perl CSS Shell Other
Latest commit 2a51bc9 Feb 16, 2017 bw2 better error message
Permalink
Failed to load latest commit information.
breakpoint_search merged in breakpoint_search Feb 5, 2017
deploy added postgres config example Feb 6, 2017
docs merged in breakpoint_search Feb 5, 2017
reference_data updatde migrations Feb 7, 2017
seqr fixed dataset query Feb 13, 2017
ui Added 'Create', 'Delete' project. Refactored a few of the seqr REST A… Feb 13, 2017
xbrowse handle DP='.' Feb 15, 2017
xbrowse_server better error message Feb 16, 2017
.gitignore added ssl key directory to .gitignore Feb 5, 2017
LICENSE.txt Initial commit - starting new repo in xbrowse organization Jan 7, 2014
Makefile server => devserver Jan 4, 2017
PHENOTIPS_INTEGRATION.md move to top level May 10, 2016
README.md renamed phenotips instructions file May 10, 2016
README_for_developers.md Added in a developer code-style guide May 10, 2016
add_new_project_by_chromosomes.py --ped option, flush logs May 12, 2015
add_new_project_directory.py --ped option, flush logs May 12, 2015
add_new_project_from_ped_file.py Add default tags Aug 9, 2016
add_new_project_from_vcf_and_ped.py Add default tags Aug 9, 2016
add_new_project_from_xls_file.py remove old command Nov 28, 2016
collect_static.sh use python2.7 Jul 24, 2016
delete_project.py Utility script for deleting projects Apr 25, 2016
functional_tests.py Adding back some old functional tests and updating README with instru… Dec 1, 2014
manage.py utility scripts for running the several commands neeeded to load a pr… Mar 23, 2015
requirements.txt updated python dependencies and settings file locations to simplify i… Jan 25, 2017
server.js another iteration of CaseReview UI Nov 28, 2016
settings.py Merge branch 'feature-refactor_ui_to_use_react.js' of github.com:maca… Feb 5, 2017
setup.py Updating setup.py; about to un-deprecate this repo Jun 11, 2014
shell.py add project, family, individual to context Jan 2, 2017
wsgi.py Using DjangoWhiteNoise to fixed Django static file handling when DEBU… Mar 21, 2016

README.md

seqr

seqr is a software package for working with next generation sequencing data, specifically in the context of studying rare genetic diseases.

This package contains the analysis code that powers the seqr website, but we welcome anyone wishing to set up their own private instance of seqr.

Please Note: This package is in active development, and the API is extremely unstable. We suggest you contact us if you want to build on this repo.

Installation Instructions

Development Plans

Current big-picture refactoring plans include:

  • refactor meta-data schema to better support multiple samples per individual (eg. for individuals that have both WGS and whole exome variant calls).
  • refactor the UI to use React.js
  • move from mongodb to a different backend that's better-optimized for our requirements (currently investigating open-source Apache tools like Solr, as well as managed cloud databases)