Repository and SOP for the Paleogenetics and Vegetation Modelling Group at the University of Bern. All pipelines and scripts are created specificly for this group.
SOP directory houses all relevant instructions for lab work.
All instructions for bioinformatics are found in the Instructions directory.
All scripts are found in the Scripts folder. This is the backup for all scripts in case irreversible changes are made to the version found on UBELIX.
Scripts are found in the following folder in our workspace on UBELIX:
cd $WORKSPACE/references/scriptsFollow the instructions in the UBELIX Starter Kit to create an account on UBELIX (UniBe HPC) and access the group's database
You can connect to the group server where the majority of the bioinfomatic files are are housed by going to Finder>Windows>Connect to Servers and then type in the following link:
smb://resstore.unibe.ch/ips_pal
This can also be done with the shortcut ⌘ K. It may ask you to give your login infomation to your UniBE Staff account. The username is the string of letters and numbers that identify you on the HPC, which should be found in the account activation email.
Similarly, you can also connect to the Group's server where the majority of written work is housed:
smb://nas-ips.unibe.ch/ips/Groups/Palaeo
You can also connect to your own server:
smb://nas-ips.unibe.ch/ips/Users/<Username>
Warning
The Username here is not the same as your email name, this is the HPC username.
We have opted to create our own pipeline for aDNA processing.
🚧 Our Pipeline is currently under construction.
Relevent information will appear here.