How do I download my sequencing data?

We do deliver sequencing data via two portals: SLIMS for Illumina data and BioShare for PacBio data.  Both portals offer secure access to the data an support several download protocols.

Since high throughput sequencing data files tend to be big it is recommended to download the data by running the “wget” command line tool (built-in on Unix/Linux/Cygwin). Wget can easily be added to Windows10 as part of bash and is also available for other Windows systems and MACs (multiple install options).  There is also an easy graphical user interface version available for Windows.

The emails that will notify you about new sequencing data on SLIMS will contain instructions.  In BioShare the instructions for several download protocols are integrated in the user interface. BioShare will automatically generate the download commands for you.

For  SLIMS a wget command like the following will be used to download all files into your current working directory. :
wget -r -nH -nc -np -R index.html*    "http://slims.bioinformatics.ucdavis.edu/Data/Your_RANDOM_STRING/" &

You can also download the files with your webbrowser (clicking the links) or better with a download manager (e.g for Firefox https://addons.mozilla.org/en-US/firefox/addon/downthemall/ )

RSYNC download is possible for both SLIMS and BioShare. Please contact Adam Schaal for assistance with the SSH keys.


Category: 06 Sequencing Data

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