DEPENDENCIES

You will need the following software:

• SPAdes (3.8.0)
• [QUAST (4.1)] (http://bioinf.spbau.ru/quast)
• [NCBI_blast + (2.2.3)] (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
• [Bedtools (2.25)] (http://bedtools.readthedocs.io/en/latest/)
• [R (3.2.5)] (https://www.r-project.org/)
• [Bowtie 2 (2.2.4)] (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
• [SAMtools (1.2)] (http://samtools.sourceforge.net/)
• [FastQC (0.11.3)] (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
• [Trimmomatic (0.33)] (http://www.usadellab.org/cms/?page=trimmomatic)
• [twoBitToFa] (https://genome.ucsc.edu/goldenpath/help/twoBit.html)

All these dependencies must be included in your $PATH for the pipeline to work without editing the code.