A program to run prokaryote genome assembly for PATRIC.
Given a list of raw read files the code will run either SPAdes or Canu.
SPAdes is run if the reads are Illumina or IonTorrent (short reads).
Canu is run if the reads are PacBio or Oxford Nanopore (long reads).
If a mix of long reads and short reads is given, SPAdes will be run with long reads used to order contigs into scaffolds.
The Trimmomatic package is included. It is run if "--runTrimmomatic" is specified. A symbolic link to the jar file is made as "trimmomatic.jar". Can be specified as argument "--trimmomatic_jar" The Illumina adapters are concatenated into a file "illumina_adapters.fa".
The Quast program (http://quast.sourceforge.net/) is referenced, but not yet included. The path to quast.py can be set by argument "--quast_path".