title: A biologist's guide to de novo genome assembly using next-generation sequence data: A test with fungal genomes.
abstract: We offer a guide to de novo genome assembly using sequence data generated by the Illumina platform for biologists working with fungi or other organisms whose genomes are less than 100Mb 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.
authors.affiliation: Faculty of Forestry, University of British Columbia, Vancouver, B.C., Canada V6T 1Z4.
authors.forename: Sajeet
authors.initials: S
authors.lastname: Haridas
authors.forename: Colette
authors.initials: C
authors.lastname: Breuill
authors.forename: Joerg
authors.initials: J
authors.lastname: Bohlmann
authors.forename: Tom
authors.initials: T
authors.lastname: Hsiang
mesh_terms: D001431:Bacteriological Techniques; D002874:Chromosome Mapping; D040481:Genome Components; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D013677:Medical Laboratory Science; D055155:Ophiostomatales / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013223:Statistics as Topic