Supersplat-spliced RNA-seq alignment

被引:26
作者
Bryant, Douglas W., Jr. [1 ,2 ,3 ]
Shen, Rongkun [1 ,2 ]
Priest, Henry D. [1 ,2 ]
Wong, Weng-Keen [3 ]
Mockler, Todd C. [1 ,2 ]
机构
[1] Oregon State Univ, Dept Bot & Plant Pathol, Corvallis, OR 97331 USA
[2] Oregon State Univ, Ctr Genome Res & Biocomp, Corvallis, OR 97331 USA
[3] Oregon State Univ, Dept Elect Engn & Comp Sci, Corvallis, OR 97331 USA
基金
美国国家科学基金会;
关键词
D O I
10.1093/bioinformatics/btq206
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: High-throughput sequencing technologies have recently made deep interrogation of expressed transcript sequences practical, both economically and temporally. Identification of intron/exon boundaries is an essential part of genome annotation, yet remains a challenge. Here, we present supersplat, a method for unbiased splice-junction discovery through empirical RNA-seq data. Results: Using a genomic reference and RNA-seq high-throughput sequencing datasets, supersplat empirically identifies potential splice junctions at a rate of similar to 11.4 million reads per hour. We further benchmark the performance of the algorithm by mapping Illumina RNA-seq reads to identify introns in the genome of the reference dicot plant Arabidopsis thaliana and we demonstrate the utility of supersplat for de novo empirical annotation of splice junctions using the reference monocot plant Brachypodium distachyon.
引用
收藏
页码:1500 / 1505
页数:6
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