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IMAP.pl
README.md
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README.md

IMAP

Chromosome-level genome assembler combining multiple de novo assemblies

System requirements (Tested versions)

  • Linux x64 (Tested in CentOS 7.5, Ubuntu 16.04 and Ubuntu 18.04)
  • Perl >= 5.22 or higher
  • Python (Python2: 2.4–2.7, and Python3: 3.2 and higher)
  • JAVA (build 1.8)
  • Perl modules
    • Switch
    • Parallel::ForkManager
    • Bio::TreeIO
    • YAML
    • ExtUtils::PkgConfig
    • GD
    • XML::Parser
    • XML::Parser::PerlSAX
    • XML::DOM
    • XML::DOM::XPath
    • XML::Twig
  • GCC (version 4.8)
  • BOOST (version 1.46.0)
  • libgd (version 2.1.1)
  • zlib (version 1.2.8)
  • libbz2 (version 1.0.6)
  • libncurses (version 6.0)

Installing IMAP from source codes

To install IMAP,

1. Download source
  git clone https://github.com/jkimlab/IMAP.git

2. Check & install the required perl libraries
  - Check the required perl libraries
    ./build.pl --check

  - Install the required perl libraries

3. Install IMAP package
    ./build.pl --install

To uninstall IMAP,

    ./build.pl --uninstall

Installing IMAP using docker

To install IMAP,

1. Install docker (https://docs.docker.com/install/linux/docker-ce/ubuntu)
    curl -fsSL https://get.docker.com/ | sudo sh
    sudo usermod -aG docker $USER 	# adding user to the “docker” group

2. Download source
  git clone https://github.com/jkimlab/IMAP.git
  
3. Build image using Dockerfile 
  - Change to the directory where Dockerfile is located.
    docker build -t [image_name] .

4. Run by docker
  - Run image and create container
    docker run -it [image_name] /bin/bash

Running IMAP with example dataset

  • Required approximately 60GB empty disk space

     ./build.pl --example
      cd IMAP_EX
      bash CMD
    

Running IMAP

To run IMAP, you need to prepare a parameter file.

  • parameter file

    You can use multiple sequencing read libraries, and one or more outgroup species.

     ############################################################
     ## Sequencing read library information
     ############################################################
     ### Average insert sizes
     ### Standard deviation of insert sizes
     ### Path of read files (.fq(.gz))
     ##### [Paired-end reads] p1, p2
     ##### [Mate-pair reads] m1, m2
     [LIB]
     insertSize	[(integer) insert size]
     insertSizeSD	[(integer) SD of insert size]
     p1	path of forward read          (ex. [path]/read1.1.fq)
     p2	path of reverse read          (ex. [path]/read1.2.fq)
     p1	path of forward read          (ex. [path]/read2.1.fq)
     p2	path of reverse read          (ex. [path]/read2.2.fq)
    
     [LIB]
     insertSize	[(integer) insert size]
     insertSizeSD	[(integer) SD of insert size]
     m1	path of forward read          (ex. [path]/read3.1.fq.gz)
     m2	path of reverse read          (ex. [path]/read3.2.fq.gz)
    
     ############################################################
     ## General assembly parameters
     ############################################################
     ## Minimum length of contigs
     MinContigLength	[(integer) minimum length of contigs]
     ## Kmer size for de novo assembly
     Kmer	[(integer) kmer]
     ### Maximum read length for SOAPdenovo2
     MaxReadLength	[(integer) maximum read length]
    
     ############################################################
     ## RACA & DESCHRAMBLER parameters
     ############################################################
     ## You can use the outrgroup more than one, but the names must be different.
     Reference	[(string) name]	[path of sequence file (.fa)]          (ex. S288C  [path]/S288C.fa)
     Outgroup	[(string) name]	[path of sequence file (.fa)]          (ex. dairenensis [path]/Saccharomyces_dairenensis.fa)
     ### Tree must contain the names of a reference, target(s) and outgroup(s) (newick format)
     TREE	[path of tree (must be in newick format)]          (ex. [path]/tree.nwk)
     ### Synteny resolution
     Resolution	[(integer) synteny resolution]
    
     ############################################################
     ## Error correction parameters 
     ############################################################
     IterationNumber	[(integer) the number of iteration]
    

Then, you can use the 'IMAP' perl script.

Usage:  ./IMAP.pl -t [threads] -p [parameter file] -o [out directory]

Options:
    --threads|-t <integer> Number of threads (default: 1)
    --params|-p <filename> Parameter file
    --outdir|-o <filename> Output directory (default: ./IMAP_RESULT)
    --help|-h Print usages
    
Simple examples:
    ./IMAP.pl -t 40 -p param.txt -o ./IMAP_RESULT

Included third party tools

Contact

bioinfolabkr@gmail.com

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