Ngless is a domain-specific language for NGS (next-generation sequencing data) processing.

Note: This is pre-release software, currently in beta (testing) It is stable enough to use, but there may still be some (minor) changes before an official release. For questions, you can also use the ngless mailing list.

ngless "0.0"
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})

See the install documentation for more information.

One of the simplest ways to install NGLess is through bioconda:

conda install -c bioconda ngless 

You can get a statically linked version of NGless 0.5 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 http://ngless.embl.de/releases/ngless-0.5.1-Linux64
chmod +x ngless-0.5.1-Linux64
./ngless-0.5.1-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.

Installing/compiling from source is also possible. Clone http://github.com/luispedro/ngless

stack is highly recommended. Install it and running make should (1) download all dependencies with the correct versions and (2) build ngless. It will perform this task in its own sandbox so it will not interfere with any other work.

You should also have gcc installed (or another C-compiler).

The following sequence of commands should download and build the software

git clone https://github.com/luispedro/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>

• Full documentation
• Frequently Asked Questions (FAQ)
• ngless mailing list

• Luis Pedro Coelho (email: [email protected]) (on twitter: @luispedrocoelho)
• Paulo Monteiro
• Renato Alves
• Ana Teresa Freitas
• Peer Bork