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.