In this section

wormbase-ws269 cactus-hal

This alignment has been generated in Ensembl Metazoa release 63.

API access

This alignment set can be accessed using the Compara API via the Bio::EnsEMBL::DBSQL::MethodLinkSpeciesSetAdaptor using the method_link_type "CACTUS_HAL" and the species_set_name "collection-wormbase-ws269".

HAL configuration

HAL alignments require further configuration. See the instructions in our README.

SpeciesAssemblyGenome length (bp)Genome coverage (bp)Genome coverage (%)
Caenorhabditis elegans (Nematode, N2) (Caenorhabditis elegans)WBcel235100,286,40136,945,67836.84
Caenorhabditis brenneri (Nematode) (Caenorhabditis brenneri)C_brenneri-6.0.1b190,369,72154,858,83628.82
Caenorhabditis briggsae (Nematode) (Caenorhabditis briggsae)CB4108,384,16539,891,55836.81
Caenorhabditis japonica (Nematode) (Caenorhabditis japonica)C_japonica-7.0.1166,256,19129,120,79717.52
Pristionchus pacificus (Nematode, PS312) (Pristionchus pacificus)El_Paco_fix158,500,3968,395,3505.30
Strongyloides ratti (Threadworm) (Strongyloides ratti)S_ratti_ED321_v5_0_443,166,8515,797,33313.43
Onchocerca volvulus (Nematode, O. volvulus Cameroon isolate) (Onchocerca volvulus)ASM49940v296,427,77963,249,36065.59
Brugia malayi (Nematode, FR3) (Brugia malayi)Bmal-4.088,235,79763,427,72071.88
Trichuris muris (Nematode) (Trichuris muris)TMUE3.0111,837,6423,761,5883.36

Cactus coverage calculation

Cactus coverage values are obtained from the output of halAlignmentDepth (Hickey et al. 2013), then aggregated per genome.