De novo assembled contigs

Trinity predicted denovo transcripts. The FASTQ sequence reads were assembled using Trinity which is specifically designed for <i>de novo </i>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.