AR Bank scripts

Bin, lib, and script dependencies:

• Biopython
• Bandage
• BBTools
• BLAST+
• c-SSTAR
• Kraken
• mlst
• Prokka
• QUAST
• QualAssessCleanSeqs.bash
• QualAssessRawSeqs.bash
• RNAmmer
• SPAdes
• summarize_kraken-report.sh
• Trimmomatic

Ref sequences and database dependencies:

• PhiX genome (FastA format)
• Illumina adapter sequences (FastA format)
• ARG-ANNOT AR database (SRST2-formatted FastA)
• plasmids database (FastA format)
• a single full-length 16S rRNA gene sequence (FastA format)

On SGE cluster:

module load Bandage/0.7.1 bbmap trimmomatic/0.35 kraken/0.10.5 SPAdes/3.6.2 quast/2.3 ncbi-blast+/2.2.30 prokka/1.8 rnammer/1.2 Python/2.7.3

Example local installation:

brew tap homebrew/science && brew update
brew install bbmap blast bowtie2 kraken mlst prokka quast rnammer spades trimmomatic
brew tap tseemann/homebrew-bioinformatics-linux && brew update
brew install bandage
pip install -U pip && pip install biopython
cd $HOME
git clone https://github.com/chrisgulvik/AR_Bank_scripts.git
echo 'export PATH="$PATH:$HOME/AR_Bank_scripts"' >> $HOME/.bash_profile
gunzip ~/AR_Bank_scripts/DBs/*.gz
echo 'export AR_BANK_DBs="$HOME/AR_Bank_scripts/DBs"' >> $HOME/.bash_profile
git clone https://github.com/chrisgulvik/c-SSTAR.git
echo 'export PATH="$PATH:$HOME/c-SSTAR"' >> $HOME/.bash_profile
git clone https://github.com/chrisgulvik/genomics_scripts.git
echo 'export PATH="$PATH:$HOME/genomics_scripts"' >> $HOME/.bash_profile
git clone https://github.com/chrisgulvik/summarize_kraken_data.git
echo 'export PATH="$PATH:$HOME/summarize_kraken_data"' >> $HOME/.bash_profile
source ~/.bash_profile