Whole genome sequencing of Drosophila affinis
Whole genome sequencing of Drosophila affinis, line no. 0141.2 using Illumina GAIIX, through a collaboration of the Institute of Evolutionary Biology, University of Edinburgh, UK and the Institute of Population Genetics, Vetmeduni, Vienna, Austria
The D. affinis genome was sequenced and assembled in collaboration between the  Institute of Evolutionary Biology, University of Edinburgh, UK (S. Marion de Procé and B. Charlesworth) and the Institute of Population Genetics, Vetmeduni, Vienna, Austria (N. Palmieri and Prof. C. Schloetterer). Drosophila affinis females from the Nebraska line no. 0141.2 from the Drosophila Species Resource Center were used for the genome sequencing. The reads were obtained by Illumina GAIIX using two lanes of paired-end reads, one with 310 bp inserts (2 x 101 bp reads + 108 bp gap between reads) and one with 630 bp inserts (2 x 101 bp reads + 428 bp gap between reads). The lane with shorter inserts had 42,657,732 pairs of reads (x 2 = 85,315,464 (read 1+2)), and the lane with longer inserts had 39,630,082 pairs of reads (x 2 = 79,260,164 (read 1+2)). We first trimmed the reads to a quality threshold of 20?. We used CLC-Bio to perform a de novo assembly, then mapped the reads again onto the obtained contigs, and finally assembled the contigs into chromosomes and annotated genes based on the D. pseudoobscura genome annotation using the Exonerate software.
The D. affinis genome was sequenced and assembled in collaboration between the  Institute of Evolutionary Biology, University of Edinburgh, UK (S. Marion de Procé and B. Charlesworth) and the Institute of Population Genetics, Vetmeduni, Vienna, Austria (N. Palmieri and Prof. C. Schloetterer). Drosophila affinis females from the Nebraska line no. 0141.2 from the Drosophila Species Resource Center were used for the genome sequencing. The reads were obtained by Illumina GAIIX using two lanes of paired-end reads, one with 310 bp inserts (2 x 101 bp reads + 108 bp gap between reads) and one with 630 bp inserts (2 x 101 bp reads + 428 bp gap between reads). The lane with shorter inserts had 42,657,732 pairs of reads (x 2 = 85,315,464 (read 1+2)), and the lane with longer inserts had 39,630,082 pairs of reads (x 2 = 79,260,164 (read 1+2)). We first trimmed the reads to a quality threshold of 20?. We used CLC-Bio to perform a de novo assembly, then mapped the reads again onto the obtained contigs, and finally assembled the contigs into chromosomes and annotated genes based on the D. pseudoobscura genome annotation using the Exonerate software.