Transcriptome assembly
After transcriptome sequencing we removed adaptor sequences and
low-quality reads in multiple steps using TrimGalore! v. 0.6.6
(Krueger, 2019), while iteratively examining the quantity and quality of
reads with FastQC v. 0.11.8 (Andrews, 2010). The cleaned reads
were subjected to de novo transcriptome assembly with
Agalma v. 2.0.0 (Dunn et al., 2013), which includes several
filtering procedures and ribosomal RNA removal followed by assembly with
Trinity v. 2.8.5 (Grabherr et al., 2011). We screened against
the NCBI UniVec database to identify vector contaminants and
rRNA transcripts. Subsequently, we performed a reference-free assessment
of the quality and completeness of our de novo assemblies with
TransRate v. 1.0.3 (Smith-Unna et al., 2016) combined with
BUSCO v. 3.0.1 (Simão et al., 2015).