title: HiSeq of randomly amplified viral cDNA: Ichetucknee Springs macrophytes
design: Virus particles were purified from macrophyte tissues through homogenization (bead-beating) followed by filtration (0.22 um) and nuclease treatment. Viral RNA was extracted with the RNeasy kit (Qiagen).  RNA was reverse-transcribed and amplified through sequence-independent single primer amplification (SISPA) using the SuperScript VI First Strand Synthesis System (Invitrogen) and random primers. Resulting products were cleaned using the AMPure XP Purification system and sheared using a Covaris instrument. NGS libraries were prepared using the Accel-NGS 1S Plus DNA Library Kit for Illumina Platforms (Swift Biosciences) and pair-end sequenced on a HiSeq platform. Raw sequence files were trimmed with Trimmomatic version 0.36.0. We noticed that libraries were contaminated with Turtlegrass virus X (TVX; accession number MH077559). Therefore, TVX sequences were removed from all analyses.