Available Reference Genomes

NGLess provides builtin support for the most widely used model organisms (human, mouse, yeast, C. elegans, …; see the full table below). This makes it easier to use the tool when using these organisms as some knowledge is already built in.

Genome references available

NGLess provides archives containing data sets of organisms. Is also provided gene annotations that provide information about protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs.

The following table represents organisms provided by default:

Name	Description	Assembly	Ensembl
bosTau4	bos_taurus	UMD3.1	75
ce10	caenorhabditis_elegans	WBcel235	75
canFam3	canis_familiaris	CanFam3.1	75
dm6	drosophila_melanogaster	BDGP6	90
dm5	drosophila_melanogaster	BDGP5	75
gg5	gallus_gallus	Gallus_gallus-5.0	90
gg4	gallus_gallus	GalGal4	75
hg38.p10	homo_sapiens	GRCh38.p10	90
hg38.p7	homo_sapiens	GRCh38.p7	85
hg19	homo_sapiens	GRCh37	75
mm10.p5	mus_musculus	GRCm38.p5	90
mm10.p2	mus_musculus	GRCm38.p2	75
rn6	rattus_norvegicus	Rnor_6.0	90
rn5	rattus_norvegicus	Rnor_5.0	75
sacCer3	saccharomyces_cerevisiae	R64-1-1	75
susScr11	sus_scrofa	Sscrofa11.1	90

These archives are all created using versions 75, 85 and 90 of Ensembl.

Automatic installation

The builtin datasets are downloaded the first time they are used and stored in a References subdirectory of the NGLess data directory:

• the global data directory (<prefix>/share/ngless/data, where <prefix> is the directory containing bin/ngless; this is normally the case for a conda or pixi install) if it is writable, so that the data is shared by everyone using that installation;

• otherwise, the user data directory (by default, $HOME/.local/share/ngless/data).

Both locations can be changed in the configuration (global-data-directory and user-data-directory).

Manual installation

It is possible to install data sets before running any script (e.g., on a machine with network access, before running on compute nodes that do not have it). For example, to install the bos taurus reference, use the following command:

$ ngless --install-reference-data bosTau4

This uses the same location rules as above: if the global data directory is writable (e.g., when running as the user who owns the installation, or with sudo), the dataset will be available for all users of that installation.

If the reference is already installed, nothing is downloaded. Otherwise, a progress bar is displayed while downloading.