Name __________________________________
-
Launch a
c4.2xlarge
instance. (2 points) -
Update your machine and install the software (
build-essential
andgit
) usingapt-get
just like we did in lab 2,3,4,5,6,7,8,9. (3 points) -
Install
LinuxBrew
andgcc
andspades
andhmmer
and thenblast
andbusco
like lab 9. (2 points) -
Download the datasets located here:
https://s3.amazonaws.com/macmanes_share/smallreads.2.fq.gz
andhttps://s3.amazonaws.com/macmanes_share/smallreads.1.fq.gz
. (3 points) -
Assemble the dataset using Spades and a kmer value of 39 (10 points)
-
Run BUSCO on the dataset like we did in lab 9, and REPORT THE NUMBER of complete orthologs you assembled. (10 points)