How do I run the BAM and CRAM download scripts?

The BAM and CRAM download scripts require wget. Once you have wget, follow the instructions at the top of the scripts.

Mac OS or Linux

wget can be obtained using homebrew on Mac OSX. Install homebrew, then type:

brew install wget


Install Cygwin. Then install the wget package.

How do I use the API?

The Application Programming Interface (API) can be used to access the CeNDR database and make a variety of queries. The API documentation details the types of queries you can make and provides examples in a variety of languages. If you are unfamiliar with APIs and how they work, I recommend taking a look at this guide.

R can be used to make queries to the API. See the examples below:

Fetch a dataframe of strain data

df <- fromJSON("https://elegansvariation.org/api/strain")

Fetch all strains for a given isotype

CB_strains <- fromJSON("https://www.elegansvariation.org/api/strain/isotype/CB4856")

How do I cite CeNDR?

Please use the citation below.

CeNDR, the Caenorhabditis elegans natural diversity resource
Cook DE, Zdraljevic S, Roberts JP, Andersen EC
(2016 Oct 3) Nucleic Acids Research [ Article on Nucleic Acids Research | DOI | Pubmed ]

Or use this bibtex entry

  title={CeNDR, the Caenorhabditis elegans natural diversity resource},
  author={Cook, Daniel E and Zdraljevic, Stefan and Roberts, Joshua P and Andersen, Erik C},
  journal={Nucleic acids research},
  publisher={Oxford University Press}