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MEGAHIT

BioConda Install Build Status codecov

MEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.

News: try v1.2.x!

MEGAHIT v1.2.x (beta) is released. Compared to v1.1.x, its changes include

  • faster and more memory-efficient than before, by using BMI2 instructions, sparsepp and xxhash
  • refactored with C++11 features
  • use CMake to build the project
  • removal of GPU support

Please follow the instructions in Getting Started to try this new version. Past versions can be found at the release page.

Getting Started

Running with Linux binaries or docker images (recommended)

wget https://github.com/voutcn/megahit/releases/download/v1.2.2-beta/MEGAHIT-1.2.2-beta-Linux-static.tar.gz
tar zvxf MEGAHIT-1.2.2-beta-Linux-static.tar.gz
cd MEGAHIT-1.2.2-beta-Linux-static/bin/
./megahit --test  # run on a toy dataset
./megahit -1 YOUR_PE_READ_1.gz -2 YOUR_PE_READ_2.fq.gz -o YOUR_OUTPUT_DIR

You can also run MEGAHIT with its docker images.

# in the directory with your input reads
docker run -v $(pwd):/workspace -w /workspace --user $(id -u):$(id -g) vout/megahit \
  megahit -1 YOUR_PE_READ_1.gz -2 YOUR_PE_READ_2.fq.gz -o YOUR_OUTPUT_DIR

Building from source

Prerequisites

  • For building: zlib, cmake >= 2.8, g++ >= 4.8.4
  • For running: gzip and bzip2
git clone https://github.com/voutcn/megahit.git
cd megahit
git submodule update --init
mkdir build && cd build
cmake .. -DCMAKE_BUILD_TYPE=Release  # add -DCMAKE_INSTALL_PREFIX=YOUR_PREFIX if needed
make -j4
make simple_test  # will test MEGAHIT with a toy dataset
# make install if needed

Usage

To run MEGAHIT with default parameters:

megahit -1 YOUR_PE_READ_1.fq.gz -2 YOUR_PE_READ_2.fq.gz -r YOUR_SE_READ.fq.gz -o YOUR_OUTPUT_DIR

If you did not install Megahit to your PATH, just run Megahit with full-path, e.g.

/PATH/TO/MEGAHIT/build/megahit

To see the full manual of Megahit, run the program without parameters or with -h.

Also, our wiki may be helpful.

Publications

  • Li, D., Liu, C-M., Luo, R., Sadakane, K., and Lam, T-W., (2015) MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, doi: 10.1093/bioinformatics/btv033 [PMID: 25609793].
  • Li, D., Luo, R., Liu, C.M., Leung, C.M., Ting, H.F., Sadakane, K., Yamashita, H. and Lam, T.W., 2016. MEGAHIT v1.0: A Fast and Scalable Metagenome Assembler driven by Advanced Methodologies and Community Practices. Methods.

License

This project is licensed under the GPLv3 License - see the LICENSE file for details