Ngless is a domain-specific language for
NGS (next-generation sequencing data) processing.
For questions and discussions, please use the NGLess mailing list.
If you are using NGLess, please cite:
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language by Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork, Microbiome (2019) https://doi.org/10.1186/s40168-019-0684-8
ngless "1.5"
input = fastq(['ctrl1.fq','ctrl2.fq','stim1.fq','stim2.fq'])
input = preprocess(input) using |read|:
read = read[5:]
read = substrim(read, min_quality=26)
if len(read) < 31:
discard
mapped = map(input,
reference='hg19')
write(count(mapped, features=['gene']),
ofile='gene_counts.csv',
format={csv})
For more information, check the docs. We also have a YouTube tutorial on how to use NGLess and SemiBin together (but you can learn to use NGLess independently of SemiBin).
See the install documentation for more information.
The recommended way to install NGLess is through bioconda:
conda install -c bioconda ngless
Alternatively, a docker container with NGLess is available at docker hub:
docker run -v $PWD:/workdir -w /workdir -it nglesstoolkit/ngless:1.5.0 ngless --version
Adapt the mount flags (-v) as needed.
You can download a statically linked version of NGless 1.5.0
This should work across a wide range of Linux versions (please report any issues you encounter):
curl -L -O https://github.com/ngless-toolkit/ngless/releases/download/v1.5.0/NGLess-v1.5.0-Linux-static-full
chmod +x NGLess-v1.5.0-Linux-static-full
./NGLess-v1.5.0-Linux-static-full
This downloaded file bundles bwa, samtools and megahit (also statically linked).
Installing/compiling from source is also possible. Clone https://github.com/ngless-toolkit/ngless
The simplest way to get an environment with all the dependencies is to use conda:
conda create -n ngless
conda activate ngless
conda config --add channels conda-forge
conda install stack cairo bzip2 gmp zlib perl wget xz pkg-config make
You should have gcc installed (or another C-compiler).
The following sequence of commands should download and build the software
git clone https://github.com/ngless-toolkit/ngless
cd ngless
stack setup
make
To install, you can use the following command (replace <PREFIX> with
the directory where you wish to install, default is /usr/local):
make make
For developers who have successfully compiled and installed NGless, running the
test scripts in the tests folder would be the next line of action to have the
output of sample test cases.
cd tests
Once in the tests directory, select any of the test folders to run NGless.
For example, here we would run the regression-fqgz test:
cd regression-fqgz
ngless ungzip.ngl
After running this script open the newly generated folder ungzip.ngl.output_ngless and view the template in the index.html file.
For developers who have done this much more datasets for testing purposes can be referenced and used by reading these documentation links: Human Gut Metagenomics Functional & Taxonomic Profiling Ocean Metagenomics Functional Profiling Ocean Metagenomics Assembly and Gene Prediction
- Full documentation
- Frequently Asked Questions (FAQ)
- ngless mailing list
- What's new log
- NGless 1.5.0 Release Documentation
- Luis Pedro Coelho (email: luispedro@big-data-biology.org) (on twitter: @luispedrocoelho)
- Paulo Monteiro
- Renato Alves
- Ana Teresa Freitas
- Peer Bork