As part of my project on describing the transcriptional impacts of predator-cue exposure in the ultra-sonic sensitive pest moth species, the fall armyworm (Spodoptera frugiperda), I am assembling my first de novo transcriptome. Having dissected the brains from 8 adult fall armyworm moths, extracted the tRNA from these tissues, and sequenced 100 bp paired-end mRNA fragments on an Illumina HiSeq 2500 machine, I am now working to assemble the highest-quality de novo transcriptome possible.
Of great interest to me is comparing the traditional tools utilized for transcriptome assembly with those tools that have been released within the past 1-2 years. These new programs, ranging from read trimmers to entire assembly algorithms, largely promise enhancements in speed while conferring little deleterious impact on, and even sometimes benefitting, assembly quality! As an additional chapter of my master's thesis, I am working to compare the transcriptome assembly quality produced from my reads between traditional and novel assembly pipelines.