https://ngless.embl.de

This is a collection of predefined ngless pipelines for processing shotgun metagenomes.

1. human-gut.ngl for human gut samples

2. marine.ngl for marine samples

3. mouse-gut.ngl for mouse gut samples

4. dog-gut.ngl for dog gut samples

5. pig-gut.ngl for pig gut samples

These are predefined, but users are encouraged to adapt them to their specific needs.

If you are using NG-meta-profiler (or any NGLess-based pipeline), 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

You need to

1. install ngless. The recommended way is through bioconda:

   conda install -c bioconda ngless

Alternatively, see the ngless documentation on how to install it.

2. copy the profiling scripts to next to where your data lives

To use the profiler, select the appropriate script (e.g., human-gut.ngl for human gut samples), put all the FastQ files from the same sample in the same directory (INPUT-DIRECTORY) with the extension .fq.gz or fastq.gz and run:

ngless human-gut.ngl INPUT-DIRECTORY OUTPUT-DIRECTORY

You can use all the ngless command line options to set options. For example, to use 8 cores, use:

ngless --threads=8 human-gut.ngl INPUT-DIRECTORY OUTPUT-DIRECTORY

If you want very verbose output:

ngless --threads=8 --trace human-gut.ngl INPUT-DIRECTORY OUTPUT-DIRECTORY

We now also provide docker containers containing all required databases on docker hub.

These images can be used directly or through the convenience script ng-meta-profiler.sh. To use ng-meta-profiler.sh simply download the script, decide which profiler to use (human-gut:1.0.0 in the example) and run:

ng-meta-profiler.sh human-gut:1.0.0 INPUT-DIRECTORY OUTPUT-DIRECTORY

which will download and analyse the specified data with the human-gut:1.0.0 profiler.

INPUT and OUTPUT should be absolute paths and INPUT should be a directory containing a metagenome as a set of files named according to the MOCAT format.

Note too that the first time you run a particular profiler, NGLess will download and index the respective databases. This is likely to take several hours (and this process does not benefit from using multiple threads). This is only necessary once. Afterwards, the index will be reused (this is what is responsible for disk space usage in the table above).

• NGLess webpage includes a section on ngless-profiler
• For questions, you can use the ngless mailing list.