TransPS：一种用于组装高质量重叠群的转录组支架后方法。
TransPS: A Transcriptome Post Scaffolding Method for Assembling High Quality Contigs.
作者信息
Liu Mingming, Adelman Zach N, Zhang Liqing
机构信息
Department of Computer Science, Virginia Tech, Blacksburg, VA.
Department of Entomology, Virginia Tech, Blacksburg, VA.
出版信息
Comput Biol J. 2014;2014. doi: 10.1155/2014/961823. Epub 2014 May 28.
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/.
动机
随着高通量测序技术的发展，转录组能够以低成本和高效率进行测序。序列组装方法已得到更新，以满足新测序技术提出的新要求。组装策略对于需要组装其实验中生成的转录组的生物学家来说很重要。然而，一些现代的从头组装策略由于序列变异会产生大量冗余重叠群，这极大地影响了下游分析和实验。这项工作提出了TransPS，一种转录组后支架构建方法，用于生成高质量的转录组。
结果
TransPS在测试转录组数据集上显示出了有前景的结果，其中冗余度至少大幅降低了50%，同时覆盖率也得到了显著提高。
可用性
网络服务器和源代码可在https://bioinformatics.cs.vt.edu/zhanglab/transps/获取。
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