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
hg19 homo_sapiens GRCh38
sacCer3 saccharomyces_cerevisiae R64-1-1
ce10 caenorhabditis_elegans WBcel235
dm3 drosophila_melanogaster BDGP5
canFam2 canis_familiaris CanFam3.1
rn4 rattus_norvegicus Rnor_5.0
bosTau4 bos_taurus UMD3.1
mm10 mus_musculus GRCm38

These archives are all created using version 75 of Ensembl.

Automatic installation

The builtin datasets are downloaded the first time they are used. They are downloaded to the user home directory and stored in home/.ngless/genomes.

Manual installation

Is possible to install data sets locally, before running any script. They can be installed in User mode or in Root mode.

To install locally (organism bos taurus), use the following command:

$ ngless --install-reference-data bosTau4

If you install as a super-user, then the dataset will be available for all users:

$ sudo ngless --install-reference-data bosTau4

When attempting to install an organism if is returned True it means that the organism is already installed, and there is no reason to install again. Otherwise, a progress bar is displayed to provide information on the download.

Data Set Structure

This section provides the technical details necessary if you wish to build your own reference for others to use automatically. For most users, it will likely be easier to directly specify the references in the ngless script.

The archives provided by NGLess contain BWA index files, the genome reference file and a gene annotation file.

Name.tar.gz
 |
 |--- Sequence
 |     |
 |     |-- BWAIndex
 |             |-- genome.fa.gz
 |             |-- genome.fa.gz.amb
 |             |-- genome.fa.gz.ann
 |             |-- genome.fa.gz.bwt
 |             |-- genome.fa.gz.pac
 |             |-- genome.fa.gz.sa
 |
 |--- Annotation
       |-- annot.gtf.gz

The basename of Description.tar.gz (Description) will have the description name of the respective organism (i.e, Mus_musculus.tar.gz).