Paramuricea biscaya reference transcriptome

Transcriptome assembly containing in situ preserved deep-sea octocorals; DWH spill impacted P. biscaya colonies and control P. biscaya colonies without visible signs of impact. mRNA library preparation was done via TruSeq RNA Library Preparation Kit at the University of Wisconsin-Madison Biotechnology Center and sequenced on an Illumina HiSeq2000 to produce 100 bp, paired-end reads. Reads were quality-assessed using FastQC and quality trimmed using Trimmomatic and Cutadapt (to remove adaptor sequences). Rcorrector and Jellyfish were used to error-correct reads. Kraken was used to remove bacterial, archaeal, and viral contamination. The remaining reads (>60 bp) were normalized and assembled using Trinity v2.4.0. Assembled contigs were again run through Kraken and analyzed with Transdecoder to identify open-reading frames (ORFs) that were at least 100 amino acids long and to predict likely coding regions. This assembly only contains isoforms with the longest ORF per trinity gene. CD-HIT was then used to further educe redundancy of the transcripts (similarity threshold of 0.95). The assembly was then annotated using dammit.