Announcing WormBase ParaSite release 8

We are pleased to announce the eighth release of WormBase ParaSite.

We now have a total of 131 genomes representing 112 species. New species in this release are Globodera rostochiensis (PRJEB13504) and Gyrodactylus salaris (PRJNA244375). A new higher-quality assembly is also available for Heligmosomoides polygyrus (PRJEB15396).

Our assembly quality widgets has been updated with new BUSCO scores. We have used BUSCO v2 and either the lineage Nematoda (for nematodes) or Metazoa (for platyhelminthes) to calculate more accurate scores.

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Planned maintenance: 26th August to 30th August 2016

Due to essential maintenance in our data centre, WormBase ParaSite will be operating an ‘at risk’ period between Friday 26th August 2016 until Tuesday 30th August 2016 (inclusive).

Whilst we will endeavour to keep the website online during this period, services may become unavailable without warning and you may experience degraded performance.  Additionally, we will not be able to respond to any help queries sent during this time, nor will you receive any acknowledgement of their receipt (they will be queued until the maintenance has completed).

Any urgent updates will be made through our Twitter account: @WBParaSite

Thank you for your understanding.

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.

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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.

 

Brugia malayi assembly update

The new release of WormBase (WS252) is the first one to feature the new and updated version 4 of the Brugia malayi assembly.

Due to additional optical mapping, as well as new long-range PacBio sequencing and additional reassembly work conducted to integrate all available data, it was possible to scaffold the 88.2Mbp assembly into 5 chromosomes as well as the symbiont Wolbachia genome. In addition 191 contigs containing unplaced sequence are available. This represents an improvement from the v3.1 assembly, that featured 94Mbp in 9779 contigs and was included in WormBase releases until WS251.

The more contiguous sequences also improved the gene set by allowing gene fragments to be assembled into complete gene structures, as well as filling gaps containing coding regions. To enable easy transitions from previous gene sets, identifiers were mapped and transferred and are accessible through the website.

Note: WormMine as well as WormBase-ParaSite are in the process of being updated to include the latest B. malayi version in their respective next release (ParaSite v6 / WormMine 252+).

Disclaimer: A publication describing in more details the improvements and new results is in preparation and the B. malayi sequencing consortium would like to reserve first publication rights until the paper has been published.

Contributors: New York University, University of Pittsburgh, Wellcome Trust Sanger Institute, Pacific Biosciences, University of Maryland, Filariasis Research Reagent Resource Center, European Bioinformatics Institute, New England Biolabs

British Society for Parasitology Spring Meeting 2016

Registration is now open for the 2016 Spring Meeting of the British Society for Parasitology (BSP), which will be held from 11th April to 13th April at Imperial College London.  A WormBase ParaSite workshop will feature as part of the schedule.

Outline Schedule: http://www.bsp.uk.net/documents/2016-springmtg-schedule/
Registration & Abstract Submission: http://www.bsp.uk.net/news-and-events/bsp-events/bsp-spring-meeting-2016-london/

If you would like to attend the WormBase ParaSite workshop, we would be grateful if you could complete this short form: http://parasite.wormbase.org/workshop.  Although advance registration is not required to attend, your responses will help us to tailor the workshop content.