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

• BWA (http://bio-bwa.sourceforge.net/)
• LASTZ (http://www.bx.psu.edu/~rsharris/lastz/)
• MaSuRCA (http://www.genome.umd.edu/masurca.html)
• SPAdes (http://bioinf.spbau.ru/spades)
• SOAPdenovo2 (https://github.com/aquaskyline/SOAPdenovo2)
• GapCloser (http://soap.genomics.org.cn/soapdenovo.html)
• RACA (https://github.com/ma-compbio/RACA)
• DESCHRAMBLER (https://github.com/jkimlab/DESCHRAMBLER)
• Pilon (https://github.com/broadinstitute/pilon)
• GATK (https://software.broadinstitute.org/gatk/)
• Picard (https://github.com/broadinstitute/picard)
• SAMtools (http://samtools.sourceforge.net/)
• Kent utilities (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/)

How to cite

Song G, Lee J, Kim J, Kang S, Lee H, Kwon D, Lee D, Lang GI, Cherry JM, Kim J. Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies. PLoS One. 2019 Aug 27;14(8):e0221858. doi: 10.1371/journal.pone.0221858.

Contact

bioinfolabkr@gmail.com