CSAR: A contig scaffolding tool using algebraic rearrangements

Kun Tze Chen, Chia Liang Liu, Shang Hao Huang, Hsin Ting Shen, Yi Kung Shieh, Hsien Tai Chiu, Chin Lung Lu

研究成果: Article同行評審

16 引文 斯高帕斯(Scopus)

摘要

Advances in next generation sequencing have generated massive amounts of short reads. However, assembling genome sequences from short reads still remains a challenging task. Due to errors in reads and large repeats in the genome, many of current assembly tools usually produce just collections of contigs whose relative positions and orientations along the genome being sequenced are still unknown. To address this issue, a scaffolding process to order and orient the contigs of a draft genome is needed for completing the genome sequence. In this work, we propose a new scaffolding tool called CSAR that can efficiently and more accurately order and orient the contigs of a given draft genome based on a reference genome of a related organism. In particular, the reference genome required by CSAR is not necessary to be complete in sequence. Our experimental results on real datasets have shown that CSAR outperforms other similar tools such as Projector2, OSLay and Mauve Aligner in terms of average sensitivity, precision, F-score, genome coverage, NGA50 and running time.

原文English
頁(從 - 到)109-111
頁數3
期刊Bioinformatics
34
發行號1
DOIs
出版狀態Published - 2018 1月 1

All Science Journal Classification (ASJC) codes

  • 統計與概率
  • 生物化學
  • 分子生物學
  • 電腦科學應用
  • 計算機理論與數學
  • 計算數學

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