A biologist's guide to de novo genome assembly using next-generation sequence data: A test with fungal genomes

We offer a guide to de novo genome assembly1 using sequence data generated by the Illumina platform for biologists working with fungi or other organisms whose genomes are less than 100 Mb in size. The guide requires no familiarity with sequencing assembly technology or associated computer programs. It defines commonly used terms in genome sequencing and assembly; provides examples of assembling short-read genome sequence data for four strains of the fungus Grosmannia clavigera using four assembly programs; gives examples of protocols and software; and presents a commented flowchart that extends from DNA preparation for submission to a sequencing center, through to processing and assembly of the raw sequence reads using freely available operating systems and software.

► Guide to the NGS (Next Generation Sequencing) technologies, particularly the Illumina sequencing platform.
► Definitions of commonly used terms in genome sequencing and assembly
► Assembly of genome sequence data for four isolates of Grosmannia clavigera using four assembly programs
► Flowchart from DNA preparation through processing and assembly of the raw sequence reads.