Transcriptome assembly from long-read RNA-seq alignments with StringTie2
Transcriptome assembly from long-read RNA-seq alignments with StringTie2
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DOI：
10.1186/s13059-019-1910-1
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发表时间：
2019-12-16
期刊：
影响因子：
12.3
通讯作者：
Pertea, Mihaela
中科院分区：
文献类型：
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作者：
Kovaka, Sam;Zimin, Aleksey, V;Pertea, Mihaela
使用最新的单分子测序仪器进行RNA测序可以产生数千个核苷酸长的读数。组合这些长读数的能力可以极大地提高长读数分析的灵敏度。在这里，我们介绍了StringTie2，一个参考指导的转录组汇编程序，可以处理短阅读和长阅读。StringTie2包括新的方法来处理长读的高错误率，并提供了处理由短读组装而成的全长超读的能力，进一步提高了短读组装的质量。StringTie2比所有同类的短读和长读分析工具更准确、更快，并且使用更少的内存。
RNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of long-read analyses. Here we present StringTie2, a reference-guided transcriptome assembler that works with both short and long reads. StringTie2 includes new methods to handle the high error rate of long reads and offers the ability to work with full-length super-reads assembled from short reads, which further improves the quality of short-read assemblies.StringTie2 is more accurate and faster and uses less memory than all comparable short-read and long-read analysis tools.