title: genome sequencing of chikungunya virus from experimental passage
design: Viral RNA was isolated using the QIAamp Viral RNA mini kit (Qiagen). cDNA was generated by reverse-transcription with Superscript II (Life Technologies) using random hexamer primers. The entire genome sequence was amplified via PCR with GoTaq DNA Polymerase (Promega) as overlapping PCR fragments 0.5-2.1 kb in length. Amplified genome fragments were purified using Ampure XP beads (Beckman Coulter), and the  fragments from each virus sample were combined to create an equamolar mixture. Libraries were prepared from the pooled viral amplicons using the Nextera XT Kit (Illumina Inc.) and the Nextera Index Kit (Illumina Inc.). Samples were sequenced in a single lane via paired-end, 75-bp read Illumina HiSeq 2500 (Illumina Inc.) at the Yale Center for Genome Analysis
library_name: Alt_Population18_Passage24