ZTPG(Zipper + Total Viewer +Plasmid Finder + Gap liner)

This is a ring-shaped genome assembler for Pacbio Reads.It uses HBAR_lpp or spari to do error-correct and then do addtional assembly.Its designed to assemble bacterial genome by one-button process and guess all plasmid.It could also use reference sequence to do reference-assist assembly and trim possible misassembly

Files

• run.py---The main wrapper script
• Config.ini ---- Configure file Please Download the total directory and then modify the Config.ini to fullfill you environment!!

Prerequirement

• Celera Assembler Please install Celera Assemberl through source file. When you install Celera Assembler, you need to modify the source code. In AS_global.h in src directory of Celera Assembler, change from

    define AS_READ_MAX_NORMAL_LEN_BITS 11
  

to

    define AS_READ_MAX_NORMAL_LEN_BITS 15

to support reads longer than 2048bp

• Bash5 Package
• pbdagcon Package or Sprai Package
• blat
• Mummer Installation

---

Download the whole directory and then unzip it.Modify Config.ini File. The detail is as follow:

    CELEDIR =    #The directory ZTPG installed
    
    NUCMER=  #nucmer location for mummer
    
    DELTAFILTER     = # delta-filter location for mummer
    
    SHOWCOORDS      = show-coords # show-coords location for mummer

    CELERAASSEMBLER = /pub/SOFTWARE/Pacbio/smrtanalysis/current/analysis/bin/wgs-7.0/Linux-amd64/bin/ #Celera Assembler binary location

    BLAT = blat # blat location

Usage

Typing run.py on the command line will give you a list of options.

• Some Typical use cases:*