ANGSD and NGSadmix activities

ANGSD and NGSadmix activities

Activities by Anders Albrechtsen, 25 January 2018

Running this activity

For this activity you will have to ssh to your instance. Get your according IP address from the website and follow the instructions of the three exercises. To visualize results in RStudio use your local browser (e.g. Chrome, Firefox or Safari), type your “[HereYourIP]:8787” and log in with the standard username and password provided.

• Activity on admixture and population structure
• Activity on PCA and MDS
• Activity on SFS, Fst, and PBS

Background information

If you want to read more about ANGSD (=Analysis of next generation Sequencing Data) or if you need to check some of the details in the manual, you can find it here . Or for specific information of specific options type $ANGSD METHODNAME for example like $ANGSD -GL or $ANGSD -doMaf .

If you want to read more about NgsAdmix or if you need to check some of the details in the manual, you can find it here .

If you want to read more about fastNGSadmix or if you need to check some of the details in the manual, you can find it here .