Announcing WormBase ParaSite release 7

Two years after the inception of WormBase ParaSite, we are pleased to announce our biggest release so far. ParaSite release 7 brings a wealth of new data and tools that we hope will ease and enhance the work of helminthologists worldwide.

WormBase ParaSite is now the repository of 128 genomes, representing 110 species. Our newest additions are the addition of twelve Trichinella species, with five different geographical isolates for Trichinella pseudospiralis. We also have added alternatives assemblies for Echinoccocus granulosus (PRJNA182977), Toxocara canis (PRJNA248777) and Wuchereria bancrofti (PRJNA275548).

Several genomes have also been updated to bring ever more high quality data to the community. WormBase core species (the five Caenorhabditis, P. pacificus, O. volvulus, B. malayi and S. ratti) have been updated to WormBase WS254. A new decontaminated annotation of Onchocerca ochengi (PRJEB1204) is available on the website. Last but not least, we’ve added comparative genomics data for our latest free-living flatworm, Macrostomum lignano (PRJNA284736), whose genome has been available on ParaSite since release 6.

assembly_stats

Among our exciting new features, we have introduced graphical overviews of genome assembly quality, pioneered by the LepBase project. These summarise some widely-used measures of assembly quality (e.g. CEGMA and BUSCO scores) in an intuitive and interactive way. The views can be seen on the landing page for each of the 128 genomes on WormBase ParaSite. The key statistics also now appear as a columns in our sortable species overview table,  allowing rapid comparison between assemblies.

Another new widget makes its debut this release. The gene expression widget is powered by Expression Atlas and, as of now, exclusive to Schistosoma mansoni (PRJEA36577). It presents the expression levels of S. mansoni genes for each stage of the parasite’s life cycle using transcriptomic data submitted to the public nucleotide archives.

What else is new on ParaSite? More tracks! New variation tracks have been imported from European Variation Archive for Schistosoma mansoni (PRJEA36577) and Strongyloides ratti (PRJEB125). We also have added RNASeq data tracks for Fasciola hepatica (PRJEB6687), Trichuris muris (PRJEB126) and Brugia malayi (PRJNA10729).

Furthermore, we introduce our very first community annotation track. Data submitted to us by community members will be displayed on this track, with due credit given for each annotation. We thank Dr Jonathan Stoltzfus for providing us with his annotations for Strongyloides stercoralis (PRJEB528).

If you have any questions, comments or feedback, please get in touch with us via our contact form.

 

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