Oxford Planarian Bioinformatics Community


Jakke Neiro1 & Nathan Kenny2

  1. Aboobaker lab, University of Oxford, jakke.neiro@zoo.ox.ac.uk

  2. Solana lab, Oxford Brookes University, nkenny@brookes.ac.uk

This site includes code, files and other resources generated by the Oxford Planarian Bioinformatics Community.

Annotation of the Schmidtea mediterranea genome

A new expression-driven annotation of the sexual planarian genome (S. mediterranea) was generated based on total RNA-seq data from this species. The annotation is based on 183 planarian RNA-seq samples (see the sample list), the PlanMine sexual genome annotation (SMESG-high), and the PlanMine sexual genome (SMESG.1).

Notebook for annotation pipline

Download S. mediterranea annotation

Annotation of the Dugesia japonica genome

Similarly to the S. mediterranea annotation, the new expression-driven D. japonica annotation was generated based on 43 RNA-seq samples (see the sample list, the Augustus-derived annotation and the genome assembly at planarian.jp.

Download D. japonica annotation

rds files of analyses presented in ACME paper

These files allow easy uploading to R of the analyses presented in the García-Castro et al. 2020 ACME paper. Download link