Crayfish Transcriptome Assembly from Illumina Sequencing

Raw reads, which were generated by the Illumina/Solexa sequencer, were first trimmed by removing adapter sequences. Low quality reads (quality scores less than 20) were trimmed and short length reads (<10 bp) were removed [45] (link)–[46] (link). The resulting high-quality reads were used in subsequent assembly. The Crayfish transcriptome was de novo assembled using Trinity software (vision 2013.02.25) with the default parameters [47] (link). In brief, three steps were performed. First, data was processed by Inchworm, in which the high-quality reads were combined to form longer fragments called contigs. Second, data was processed by Chrysalis, in which sequences were obtained by connecting contigs in such a manner that they could not be extended on either end, which resulted in de Bruijn graphs. Finally, de Bruijn graphs were further treated by Butterfly to obtain transcripts.