Chromosome-level genome assembler combining multiple de novo assemblies
- 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)
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
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
-
Required approximately 60GB empty disk space
./build.pl --example cd IMAP_EX bash CMD
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
- 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/)
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.
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