KennthShang / TarGene

TarGene

Metagenomic data provides an opportunity to discover microbial communities and their characteristics. However, many researchers are only interested in some specific species and don’t need to analyze the whole datasets.

We developed a novel pipeline named TarGene for assembling genome of interest. In this method, the functional genes are provided as reference, TarGene will then recruit more reads that belong to the same genome as the reference genes. Finally, a de Bruijn graph will be built on these recruited reads to assemble the genome sequences. We tested our pipeline using several real metagenomic datasets.

To use TarGene, you need to have two types of data. (1) read set, such as metagenomic data containing reads. (2) reference gene, which can be a gene or a related gene database. If you are using a gene database as reference, we recommand you to run our tools named Recruit Reference Program first. It will help you save a large bunch of time.

We provide two methods for installing TarGene. You can directly install these tools following the instructions below. In addition, we also provide packaged TarGene via Anaconda, which makes the installation more straightforward.

Required Dependencies

1. Samtools
2. Bowtie2
3. SPAdes

Installing the required dependencies via conda

The easiest way to install these tools is to install anaconda and add anaconda binary to your PATH:

1. Go to [Anaconda] (https://www.anaconda.com/distribution/). Choose "Linux". Then you see a title named Anaconda 2018.12 for Linux InstallerDownload. Download the .sh file by clicking the Download buttons. Both Python 3.7 and 2.7 versions are OK.
2. Bash the .sh file and install anaconda to your computer.
3. Add the anaconda to your PATH. The following is from the FAQ of Anaconda. Conda will not work until you add the PATH manually. To add the PATH manually, open a text editor and open the file .bashrc or .bash_profile from your home directory. Add the line export PATH="/<path to anaconda>/bin:$PATH" . NOTE: Replace <path-to-anaconda>\ with the actual path of your installed anaconda file.

Then you can install these tools using the commands shown below:

conda install -c bioconda samtools bowtie2 spades

Installing TarGene

To download the source code:
git clone https://github.com/KennthShang/TarGene.git

1. Install TarGene module
   This program requries the supports of C++11.

  cd TarGene
  make    

Quickstart using shell script

Use testdata as an example. Make a copy of bin/xander_setenv.sh and change path variables to be the absolute paths in your system. For your samples, you may also need to adjust the Parameters used in TarGene

The following example commands will attempt to run all the three steps "rrp", "TarGene" and "SPAdes" for the genes Hydroxylamine oxidoreductase (hao) and Ammonia monooxygenase subunit A (amoA) specified in the input param. It creates an assembly output directory "recruit50" for overlap cutoff of 50. It saves all the output in the output directory.

cd test_data
cp ../script/set_env.sh my_env.sh
# edit the parameters in my_env.sh 
bash ../script/main.sh my_env.sh "crp TarGene SPAdes"

You can also run the three steps separately, or choose the program you want to run.

bash ../script/main.sh my_env.sh "crp"
bash ../script/main.sh my_env.sh "TarGene"
bash ../script/main.sh my_env.sh "SPAdes"

Note if you want to rerun the program, you need to manually delete the corresponding files in the output directory.