The paper introduces Trinity, a novel method for de novo transcriptome reconstruction from RNA-Seq data, particularly useful when a reference genome is not available. Trinity consists of three software modules: Inchworm, Chrysalis, and Butterfly, which work sequentially to process large volumes of RNA-Seq reads. The method efficiently reconstructs full-length transcripts, including alternative splice isoforms and transcripts from recently duplicated genes, outperforming other available de novo assembly tools and performing comparably to methods relying on genome alignments. The authors evaluated Trinity on fission yeast, mouse, and whitefly (an insect with no sequenced genome) samples, demonstrating its effectiveness in recovering most annotated transcripts and resolving complex transcript structures. Trinity's performance is assessed through various benchmarks, including sensitivity, splicing pattern detection, and locus coverage, showing its robustness and accuracy in transcriptome reconstruction.The paper introduces Trinity, a novel method for de novo transcriptome reconstruction from RNA-Seq data, particularly useful when a reference genome is not available. Trinity consists of three software modules: Inchworm, Chrysalis, and Butterfly, which work sequentially to process large volumes of RNA-Seq reads. The method efficiently reconstructs full-length transcripts, including alternative splice isoforms and transcripts from recently duplicated genes, outperforming other available de novo assembly tools and performing comparably to methods relying on genome alignments. The authors evaluated Trinity on fission yeast, mouse, and whitefly (an insect with no sequenced genome) samples, demonstrating its effectiveness in recovering most annotated transcripts and resolving complex transcript structures. Trinity's performance is assessed through various benchmarks, including sensitivity, splicing pattern detection, and locus coverage, showing its robustness and accuracy in transcriptome reconstruction.