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Change Log

v1.5.2 (2020-09-07)

  • A divergent region summary track has been added to the primer indel tool.
  • Sweep haplotypes have been added to the latest release.

v1.5.1 (2020-08-30)

v1.5 (2020-08-15)

  • The primary data model has moved from isotypes to strains.
  • The backend of the site has been substantially restructured to improve maintainability.
  • A table of strains with issues has been added to the data releases page.
  • The variant data table has been removed from isotype pages.
  • New strain collection images have been added.
  • The API has been removed. It did not see a lot of usage and become cumbersome to maintain.
  • A new collaborators page has been added.
  • Software and Methods have been moved to be per-release, as the pipeline is ever-evolving.
  • Data links have been removed from isotype pages; They are still available on the release pages.
  • Reports for Alignment, Concordance, And Variant calling are now produced for all releases.
  • Publications have been updated.
  • The public mappings page was removed as our mapping infrastructure is changing.
  • A new tool for calculating heritability has been released.
  • A tool for generating primers for genotyping indels will be released soon.

Genome Browser

  • IGVjs has been upgraded and has a number of new tools.
  • A track for repeat_masker, and Dust data has been added.
  • A track for transposons from Laricchia et al. 2017 been added.
  • Tracks for divergent regions from Lee et al. 2020 have been added.

v1.3.4 (2020-02-23)

  • Logins now redirect to the previous page.
  • Fixed Github authentication issues. A public email is no longer required.

v1.3.3 (2020-02-04)

  • Fixed Google authentication issues.

v1.3.2 (2019-10-20)

  • Update Strain map background to ESRI worldmap tileset.
  • Add a publications page listing publications that have cited CeNDR.
  • Fixed a bug that broke the statistics page.
  • Updated internal software to improve security.

v1.3.1 (2019-02-17)

  • Use a natural sort for strain names on global strain map.
  • Update software versions.
  • Improvements to ordering form.
  • Add code of conduct.
  • Add issue tracker link.

v1.3.0 (2018-10-03)

  • Add interval data to reports

v1.2.9 (2018-04-15)

  • New dataset release: 20180527
  • Added collection photos.
  • Added variant counts.
  • Fixed issue with early reports missing.
  • Added variant correlation plot.

v1.2.8 (2018-03-18)

  • Fix link on data page
  • Fix error with ordering

v1.2.7 (2018-03-01)

  • Fix site error when strain URL not found.
  • Fix warning banner for users attempting to access their profile that are not logged in.
  • Update sqlite schema.

v1.2.6 (2018-02-23)

  • Fix error with v1 reports that are not significant.

v1.2.5 (2018-02-23)

  • Prevent queries on browser from exceeding 100kb and crashing the site.
  • Fix v1 report links
  • Fix LD plots on v1 reports
  • Fix homepage link
  • Fix errant API calls on gene pages
  • Fix broken link on outreach page.

v1.2.4 (2018-02-21)

  • Fix issue with the way private reports are organized.

v1.2.3 (2018-02-21)

  • Fix genome browser URLs.

v1.2.2 (2018-02-21)

  • Removed extraneous information from v2 report.

v1.2.1 (2018-02-21)

  • Quick fix for certain v2 reports that would not load properly

v1.2.0 (2018-02-21)

New Pages

  • A statistics page has been added that details strains/isotypes collected over time, visitors over time, and

Site Infrastructure

  • Added login system
  • Moved codebase to Python 3.
  • Improved robustness of forms using python module WTForms.
  • Switched database to a single SQLite flatfile + Google Datastore
  • Moved BAMs to AWS.

Mapping Pipeline

  • Moved mapping infrastructure to AWS Fargate
  • Added new description field
  • The embargo option has been dropped for publishing reports
  • Added tooltips to report allele distribution maps.
  • Mapping reports have been removed from gene pages. The new database infrastructure makes it difficult to incorporate these.


  • Add allele frequency (AF) as column on variant output.
  • Added BAMs for strains
  • Reorganized variant data table output. Variants that affect multiple transcripts are now grouped together.

Public Mappings

  • The waffle chart has been removed.


  • CRAMS files and downloads have been removed.

v1.1.2 (2017-12-05)

  • Fixed a bug preventing the download button from working properly.

v1.1.1 (2017-10-18)

  • Fixed Drawing of the Tajimas D plot on report pages.
  • Added ability to view all genotypes on the variant viewer

v1.1.0 (2017-06-16)

  • A revamped genome browser, which offers the ability to download data in a tab-delimited format (TSV).
  • The release of a larger set of strains (our 2017-05-31 set). The site now has 249 isotypes available, and a fourth set of strains.
  • The Data page has been renamed as the 'releases' page to reflect the fact that our set of genomic data continues to evolve.
  • Many other bug-fixes and minor enhancements.

v1.0.9 (2017-01-24)

  • Released transposon data.

v1.0.8 (2016-12-20)

  • Fixed issue with ordering page

v1.0.7 (2016-12-19)

  • Fixed issue with css on strain pages.

v1.0.6 (2016-12-03)

  • Added additional error checking to mapping submission page.
  • Changed submissions to run 'on demand.'

v1.0.5 (2016-12-01)

  • Fixed an issue with GWA submission.

v1.0.4 (2016-11-28)

  • Fixed an issue regarding encoding of strain meta info.

v1.0.3 (2016-11-18)

  • Fixed searching on public mappings.
  • Fixed the calendar heatmap on public mappings.
  • Fixed caching on reports.
  • Updated phenotype histogram to use plotly-js.
  • Genotypes are now shown beneath variants on the browser page. We are working on methods for exporting data.

v1.0.2 (2016-11-02)

  • Fixed an issue that prevented variant correlation tables from being output.

v1.0.1 (2016-10-18)

  • A change log has been added. You are looking at it.
  • A link to the change log was added to the homepage.
  • A link to the CeNDR paper and Nucleic Acids Research was added to the homepage.
  • Fixed an issue that prevented the phastCons track from showing on the browser.
  • Fixed sorting of news items.