Trinity

Trinity is a software tool for de novo assembly and reconstruction of full-length transcripts from RNA-Seq data without needing a reference genome. It employs an innovative approach to constructing and analyzing de Bruijn graphs to efficiently reconstruct many transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Trinity has been evaluated on various samples, such as fission yeast, mouse, and whitefly, demonstrating its ability to recover more full-length transcripts across a wide range of expression levels compared to other de novo transcriptome assemblers. The sensitivity of Trinity is comparable to methods that rely on genome alignments, making it a comprehensive solution for transcriptome reconstruction in any sample, mainly when a reference genome is unavailable or incomplete.