I have downloaded RNA-seq of an organism from SRA of NCBI. Then, I did quality control, trimming, removing contamination and de novo assembly. When I checked assessment of assembly using BUSCO, I found 20 % of BUSCO genes are in the assembly.
My question is about library preparation of the species below can affect assembly quality or I need to do additional thing apart from what I did before or not? Library: Name: Armorloricus elegans transcriptome Instrument: Illumina HiSeq 2000 Strategy: RNA-Seq Source: TRANSCRIPTOMIC Selection: PolyA Layout: PAIRED