title: Hyaloperonospora arabidopsidis Waco9 genome sequencing
design: Genomic DNA was extracted from Hpa Waco9 conidiospores using a Nucleon PhytoPure DNA extraction kit (GE Healthcare) according to the procedure of the manufacturer. A paired-end 400 bp insert size library was prepared and sequenced on Illumina Genome Analyzer II. The sequence reads were aligned in a paired end fashion to the Hpa Emoy2 v8.3 using BWA. Trailing nucleotides with a quality score of less than 10 were trimmed using the -q option. In order to maximize the number of aligned reads, unaligned reads were aligned using a more sensitive aligner, Stampy. SAMtools was used to generate a BAM file that enables visualization of the alignment with the Integrative Genomics Viewer. For correction of Hpa genome by Waco9 SNVs, genetic variations between Hpa Emoy2 and Waco9 were predicted using SAMtools. Hpa Emoy2 v8.3 genome sequence was corrected by substituting Hpa Waco9 SNVs. Insertion and deletion variations were ignored.