NGLess: NGS Processing with Less Work

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

Example

ngless "1.0"
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})

Installing

See the install documentation for more information.

Bioconda

The recommended way to install NGLess is through bioconda:

conda install -c bioconda ngless

Docker

Alternatively, a docker container with NGLess is available at docker hub:

docker run -v $PWD:/workdir -w /workdir -it nglesstoolkit/ngless:1.0.0 ngless --version

Adapt the mount flags (-v) as needed.

Linux

You can get a statically linked version of NGless 1.0.0 or a nighly build of the latest development code. This should work across a wide range of Linux versions (please report any issues you encounter):

curl -O https://ngless.embl.de/releases/ngless-1.0.0-Linux64
chmod +x ngless-1.0.0-Linux64
./ngless-1.0.0-Linux64

This download bundles bwa, samtools and megahit (also statically linked).

If you want to try one of ngless' builtin modules (motus, specI, ...) you can download the full nighly build zip file which includes them.

From Source

Installing/compiling from source is also possible. Clone https://github.com/ngless-toolkit/ngless

Dependencies

The simplest way to get an environment will all the dependencies is to use conda:

conda create -n ngless
source 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
make

To install, you can use the following command (replace <PREFIX> with the directory where you wish to install, default is /usr/local):

make install prefix=<PREFIX>

More information

Authors

Luis Pedro Coelho (email: coelho@embl.de) (on twitter: @luispedrocoelho)
Paulo Monteiro
Renato Alves
Ana Teresa Freitas
Peer Bork

TankMermaid/ngless