Sequencing Strategy & Assembly

Motivation

While there are industry standard tools for assembling Sanger-based shotgun datasets, there is currently no widely accepted method for assembling short-read (Illumina) datasets to provide accurate, contiguous, and well-scaffolded genome sequences for complex (i.e., large, repetitive) genomes. This project aims at (1) developing strategies for shotgun sequencing of complex genomes with non-Sanger technologies, and (2) accurate and complete assemblies of complex genomes from such datasets.

Results

Building on long-standing JGI efforts in genome assembly, the "meraculous" toolkit has been developed. This assembler is highly accurate in an absolute sense (no errors made) and relative to other short-read assemblers (which typically show mis-joins and other errors), and is further distinguished by high levels of parallelization in some stages and novel efficient memory usage in others. A pipeline is being developed to provide a robust and easy-to-use assembly tool for use by the plant program and other programs, as well as allow this JGI-developed algorithm to find broader usage in the next-generation sequencing community.