PgmNr M5101: Using the web-based genome browser gEVAL, to evaluate and improve the draft assemblies of 18 strains for the Mouse Genomes Project.

Authors:
W. Chow; K. Howe


Institutes
Wellcome Trust Sanger Institute, Cambridge, UK.


Abstract:

The Mouse Genomes Project used next generation sequencing technologies to sequence and assemble 16 key laboratory mouse strains and 2 wild derived mouse strains to produce a comprehensive picture of variation amongst mouse genomes.  However, like many de novo genome projects, the initial draft assemblies revealed regions of discordance and misassemblies.  

To aid in the improvement and curation of these genomes, and to incorporate new long-range datasets, the assemblies of these 18 strains were recently added to the web-based genome evaluation browser gEVAL (BioRxiv, 2016).  gEVAL has been successfully used to curate the human mouse and zebrafish reference genomes, which has later led to other reference assemblies such as rat, pig, chicken, and tasmanian devil to be included in the browser.

gEVAL provides a one-stop solution to assess the compliance of a given assembly with a multitude of available data such as the correct pairing and suitable distance of mapped clone ends, the placement of markers and cDNAs, inter-comparative alignments between assemblies, long range genome/optical mapping datasets and many more.

Having these assemblies publically accessible in gEVAL, along with a whole range of supporting datasets, allows the wider mouse research community an early, easy way of accessing and evaluating the contiguity of a region of interest and view the already available gene sets.

Furthermore, gEVAL provides a platform to assist our curation groups that are tasked with improving these assemblies and the annotation of features such as genes, in hopes that these efforts will contribute to yielding full genome sequences of quality comparable to the reference standard .

Website: http://geval.sanger.ac.uk/

BioRxiv: http://dx.doi.org/10.1101/038638 (accepted in Bioinformatics, March 2016).