Assembly QuestΒΆ

I am going to give you some data and a genome (well, 500Mb of the genome). Please assemble and use BUSCO.

** Launch an AMI. For this exercise, try a c4.8xlarge with a 200Gb EBS volume. Wow yes this is a BIG machine!!

You will need to install abyss Installing BUSCO is a bit of a PITA... Here is the way, once you have brew installed.

brew install emboss
brew install busco --without-blast --without-emboss

curl -LO
tar -zxf ncbi-blast-2.3.0+-x64-linux.tar.gz

export AUGUSTUS_CONFIG_PATH=/home/ubuntu/.linuxbrew/Cellar/augustus/3.2.2_1/libexec/config/

Download the reads They have already been trimmed for you :)..

#Paired-end data

curl -LO
curl -LO

#Mate-pair data

curl -LO
curl -LO

Use ABySS to assemble reads You have 32 threads to use! I suggest you use them all.

  1. Go to the spreadsheet:
  2. Pick a kmer and sign up for it with your name. Use this kmer in your assembly.

Evaluate your assembly data using busco You’ll need to download and un-compress the Fungal database before you run BUSCO. I’m giving you that code, but not the code for running BUSCO.. You’ll have to do that yourself...

cd $HOME
curl -LO
tar -zxf fungi_buscos.tar.gz

Add your data about the assembly

Super bonus points to anybody that maps with a different assembler e.g., SPAdes, AllPaths, Velvet, ...


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