Assembly Quest¶

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 ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.3.0/ncbi-blast-2.3.0+-x64-linux.tar.gz
tar -zxf ncbi-blast-2.3.0+-x64-linux.tar.gz
PATH=$HOME/ncbi-blast-2.3.0+/bin:$PATH

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 https://s3.amazonaws.com/macmanes_share/ERR1328557_1.fastq.gz
curl -LO https://s3.amazonaws.com/macmanes_share/ERR1328557_2.fastq.gz

#Mate-pair data

curl -LO https://s3.amazonaws.com/macmanes_share/ERR1328558_1.fastq.gz
curl -LO https://s3.amazonaws.com/macmanes_share/ERR1328558_2.fastq.gz

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

Go to the spreadsheet: https://docs.google.com/spreadsheets/d/1Lncy90LS80_QDRak4Azrx_nvip8vcQvwDU7Su_gf3XY/edit?ts=57aca0ad#gid=0
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 http://busco.ezlab.org/files/fungi_buscos.tar.gz
tar -zxf fungi_buscos.tar.gz

Add your data about the assembly

https://docs.google.com/spreadsheets/d/1Lncy90LS80_QDRak4Azrx_nvip8vcQvwDU7Su_gf3XY/edit?ts=57aca0ad#gid=0

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

TERMINATE YOUR INSTANCE!!!

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.