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https://github.com/voutcn/megahit
Ultra-fast and memory-efficient (meta-)genome assembler
https://github.com/voutcn/megahit
bioinformatics data-structures genome-assembly genomics metagenomics succinct
Last synced: 3 months ago
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Ultra-fast and memory-efficient (meta-)genome assembler
- Host: GitHub
- URL: https://github.com/voutcn/megahit
- Owner: voutcn
- License: gpl-3.0
- Created: 2014-09-25T10:29:18.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2024-04-30T05:02:24.000Z (7 months ago)
- Last Synced: 2024-06-24T01:38:41.070Z (5 months ago)
- Topics: bioinformatics, data-structures, genome-assembly, genomics, metagenomics, succinct
- Language: C++
- Homepage: http://www.ncbi.nlm.nih.gov/pubmed/25609793
- Size: 3.05 MB
- Stars: 570
- Watchers: 36
- Forks: 134
- Open Issues: 97
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
MEGAHIT
=======
[](https://anaconda.org/bioconda/megahit)
[](https://github.com/voutcn/megahit/releases)
[](https://travis-ci.org/voutcn/megahit)
[](https://codecov.io/gh/voutcn/megahit)
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.
Installation
---------------
### Conda
```sh
conda install -c bioconda megahit
```
### Guix
```sh
guix install megahit
```
### Pre-built binaries for x86_64 Linux
```sh
wget https://github.com/voutcn/megahit/releases/download/v1.2.9/MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz
tar zvxf MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz
cd MEGAHIT-1.2.9-Linux-x86_64-static/bin/
./megahit --test # run on a toy dataset
./megahit -1 MY_PE_READ_1.fq.gz -2 MY_PE_READ_2.fq.gz -o MY_OUTPUT_DIR
```
### Pre-built docker image
``` sh
# in the directory with the input reads
docker run -v $(pwd):/workspace -w /workspace --user $(id -u):$(id -g) vout/megahit \
megahit -1 MY_PE_READ_1.fq.gz -2 MY_PE_READ_2.fq.gz -o MY_OUTPUT_DIR
```
### Building from source
#### Prerequisites
- For building: zlib, cmake >= 2.8, g++ >= 4.8.4
- For running: gzip and bzip2
```sh
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=MY_PREFIX if needed
make -j4
make simple_test # will test MEGAHIT with a toy dataset
# make install if needed
```
Usage
-----
### Basic usage
```sh
megahit -1 pe_1.fq -2 pe_2.fq -o out # 1 paired-end library
megahit --12 interleaved.fq -o out # one paired & interleaved paired-end library
megahit -1 a1.fq,b1.fq,c1.fq -2 a2.fq,b2.fq,c2.fq -r se1.fq,se2.fq -o out # 3 paired-end libraries + 2 SE libraries
megahit_core contig2fastg 119 out/intermediate_contigs/k119.contig.fa > k119.fastg # get FASTG from the intermediate contigs of k=119
```
The contigs can be found `final.contigs.fa` in the output directory.
### Advanced usage
- `--kmin-1pass`: if sequencing depth is low and too much memory used when build the graph of k_min
- `--presets meta-large`: if the metagenome is complex (i.e., bio-diversity is high, for example soil metagenomes)
- `--cleaning-rounds 1 --disconnect-ratio 0`: get less pruned assembly (usually shorter contigs)
- `--continue -o out`: resume an interrupted job from `out`
To see the full manual, run `megahit` without parameters or with `-h`.
Also, our [wiki](https://github.com/voutcn/megahit/wiki) may be helpful.
### Examples
There is an example of a real assembly on this [wiki page](https://github.com/voutcn/megahit/wiki/An-example-of-real-assembly)
and its corresponding [interactive Jupyter notebook](https://biotutorials.org/megahit). Contributed by Noah Lebovic (@lebovic).
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 \[PMID: [25609793](http://www.ncbi.nlm.nih.gov/pubmed/25609793)\].
- 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](LICENSE) file for details