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High-throughput sequencing of mRNAs has revolutionized our ability for transcripts reconstruction. However, the massive size of short reads makes de novo transcripts assembly an algorithmic challenge.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>We develop a novel radical framework, called DTA-SiST, for de novo transcriptome assembly based on suffix trees. DTA-SiST first extends contigs by reads that have the longest overlaps with the contigs\u2019 terminuses. These reads can be found in linear time of the lengths of the reads through a well-designed suffix tree structure. Then, DTA-SiST constructs splicing graphs based on contigs for each gene locus. Finally, DTA-SiST proposes two strategies to extract transcript-representing paths: a depth-first enumeration strategy and a hybrid strategy based on length and coverage. We implemented the above two strategies and compared them with the state-of-the-art de novo assemblers on both simulated and real datasets. Experimental results showed that the depth-first enumeration strategy performs always better with recall and also better with precision for smaller datasets while the hybrid strategy leads with precision for big datasets.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Conclusions<\/jats:title>\n<jats:p>DTA-SiST performs more competitive than the other compared de novo assemblers especially with precision measure, due to the read-based contig extension strategy and the elegant transcripts extraction rules.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s12859-019-3272-9","type":"journal-article","created":{"date-parts":[[2019,12,24]],"date-time":"2019-12-24T09:02:35Z","timestamp":1577178155000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["DTA-SiST: de novo transcriptome assembly by using simplified suffix trees"],"prefix":"10.1186","volume":"20","author":[{"given":"Jin","family":"Zhao","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haodi","family":"Feng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daming","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,12,24]]},"reference":[{"issue":"4","key":"3272_CR1","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1101\/gad.1048803","volume":"17","author":"NA Faustino","year":"2003","unstructured":"Faustino NA, Cooper TA. 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