What’s coming in Ensembl release 86

Ensembl 86 is scheduled for September 2016, highlights include:

New mouse strains

  • Annotated genome assemblies, variation data and comparative analyses of 16 different mouse strains will be included in Ensembl 86.

Updated assemblies, gene sets and annotations

  • Human: updated cDNA alignments and RefSeq import
  • Mouse: updated cDNA alignments and RefSeq import
  • Zebrafish: updated gene set and RefSeq import
  • Chicken: updating to the Galgal_5.0 assembly
  • Mouse lemur: updating to the Mmur_2.0 assembly
  • Macaque:  updating to the Mmul_8.0.1 assembly

New lincRNA data

New GRCh37 tools converted from 1000 Genomes Project

A number of tools previously developed for use in the 1000 Genomes Project browser have now been converted for use with the GRCh37 assembly in Ensembl:

  • Dataslicer tool- This tool allows you to get a subset of data from a BAM or VCF file.
  • Variation pattern finder tool- This tool allows you to identify variation patterns in a chromosomal region of interest for different individuals.
  • Forge analysis tool- This tool takes a list of variants and analyses their enrichment in functional regions from the ENCODE or Roadmap Epigenome project on a tissue specific basis.

Other updates and highlights

  • Variation and phenotype databases updates

For more details on the declared intentions, please visit our Ensembl admin site. Please note that these are intentions and are not guaranteed to make it into the release.

8 thoughts on “What’s coming in Ensembl release 86

    • No, that is unrelated to the release. As per the notice on our *.ensembl.org sites, our datacentre has been undergoing planned maintenance work this weekend; we hope to have all services back shortly.

    • Dear Anton,

      We do not currently have a fixed timeline for including the OAR4.0 genome assembly in Ensembl, but we hope to annotate it in the early part of 2017.

      Best wishes

      Ben
      Ensembl Helpdesk

    • Dear Michael,

      We have recently been updating our gene annotation pipeline to improve it’s efficiency, and we now plan to update a number of primate assemblies, including Gorilla, in the next few releases of Ensembl. We will annotate the GorGor4 assembly at first, then assess whether we will annotate the new PacBio gorilla assembly in the more distant future.

      Best wishes

      Ben
      Ensembl Helpdesk

  1. We use screenshots and links from Ensembl in our training materials and so major changes may “break” our workbook examples. I know that these release dates have some uncertainty, but approximately when in September might v86 be public?

    • Dear Paul,

      It’s great to hear that you provide your own Ensembl training. There is no fixed date for the release of Ensembl 86, but we anticipate it will be in the week beginning 26th September. We will publish a blog post with details about new features upon the release.

      If you are interested in preparing your own training materials, we have our own hosted online, that you can modify and use, on training.ensembl.org.

      Best wishes

      Ben
      Ensembl Helpdesk