De novo assembled contigs

Trinity predicted denovo transcripts. The FASTQ sequence reads were assembled using Trinity which is specifically designed for de novo assembly of transcriptomes. Trinity was run on the paired end sequences with the fixed default k-mer size of 25 and minimum contig length of 200. Assembly algorithm runs on three steps, Inchworm, Chrysalis and Butterfly. Inchworm first assembles overlapping sequences using a greedy extension and reports the unique portions of alternatively spliced transcripts (contigs). Chrysalis then clusters related contigs into components (i.e., compXXXX_c0) and models complexity using de Bruijn graphs for each of the clusters. Finally, Butterfly processes the graphs and reports subcomponents (i.e., compXXXX_c0_seq1, compXXXX_c0_seq2, etc.), roughly corresponding to genes that are made up of individual transcripts.