TransPS: A Transcriptome Post Scaffolding Method for Assembling High Quality Contigs. Academic Article uri icon

abstract

  • MOTIVATION: As the development of the high throughput sequencing technologies, transcriptome can be sequenced with a low price and high efficiency. Sequence assembly approaches have been renewed to meet the new requirements from new sequencing technologies. Assembly strategies are important for biologists who need to assemble the transcriptome generated in their experiments. However, some modern de novo assembly strategies generate a large section of redundant contigs due to sequence variations, which greatly affect downstream analysis and experiments. This work proposed TransPS, a post transcriptome scaffolding method to generate high quality transcriptomes. RESULTS: TransPS shows promising results on the test transcriptome data sets where the redundancy is greatly reduced by at least 50%, while the coverage is improved considerately. AVAILABILITY: The web server and source code are available at https://bioinformatics.cs.vt.edu/zhanglab/transps/.

published proceedings

  • Comput Biol J

altmetric score

  • 0.25

author list (cited authors)

  • Liu, M., Adelman, Z. N., & Zhang, L.

citation count

  • 13

complete list of authors

  • Liu, Mingming||Adelman, Zach N||Zhang, Liqing

publication date

  • May 2014