Submit CSP proposal
Announcements
- February 25-28, 2018
European Conference on Fungal Genetics, Haifa, Israel - March 13-16, 2018
Fungal genomics workshop @ JGI User Meeting, San Francisco, CA, U.S.A. - July 16-21, 2018
International Mycological Society Annual Meeting, San Juan, Puerto Rico
Releases
- May 6, 2024
Aspergillus carbonarius ITEM 5010 v4.1 - May 6, 2024
Scenedesmus obliquus SAG 2326 v1.0 - May 6, 2024
Entomoneis sp. UTEX 11IV18-2A FL v1.0 - May 6, 2024
Scenedesmus sp. WC-1 v1.0 - May 6, 2024
Scenedesmus dimorphus UTEX 1237 v1.0
Assembly
Sequencing fungal genomes at JGI relied initially on Sanger sequencing, and later on 454 pyrosequencing. In 2011, we again migrated to a new platform in order to reduce cost and cycle time, and all fungal genomes are now sequenced with Illumina short reads. The transition to short reads requires new assembly approaches to utiliize huge numbers of short reads.
Our current fungal assembly strategy relies on the allpaths-lg assembler developed at the Broad. Allpaths-LG is targeted to work with Illumina data and requires both a standard and a jumping library. Using this approach we have matched or exceeded the quality of earlier Sanger draft sequencing in scaffolding for two medium sized fungal genomes used in testing and validation. We are also exploring use of PacBio data for improving fungal genome assemblies.
We work closely with the JGI R&D group to develop high quality jumping libraries and to optimize the insert size of both the fragment and jumping libraries. We are also working very closely with the development team at the Broad to improve and allpaths-lg assembler. Our R&D efforts focus on investigating alternative assemblers as potentially useful tools are developed by the community.