This is a collection of predefined ngless pipelines for processing shotgun metagenomes.
human-gut.ngl
for human gut samples
marine.ngl
for marine samples
mouse-gut.ngl
for mouse gut samples
dog-gut.ngl
for dog gut samples
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
install ngless. The recommended way is through bioconda:
conda install -c bioconda ngless
Alternatively, see the ngless documentation on how to install it.
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.
Profiler | Memory | Disk space |
---|---|---|
Human | 14.7G | 18G |
Mouse | 5.1G | 6.3G |
Dog | 4.5G | 3.5G |
Pig | 10.1G | 17G |
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).