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Supersplat--spliced RNA-seq alignment

Journal Article · · Bioinformatics
 [1];  [2];  [2];  [3];  [2]
  1. Oregon State Univ., Corvallis, OR (United States). Center for Genome Research and Biocomputing. Dept. of Botany and Plant Pathology; Oregon State Univ., Corvallis, OR (United States). Dept. of Electrical Engineering and Computer Science; DOE/OSTI
  2. Oregon State Univ., Corvallis, OR (United States). Center for Genome Research and Biocomputing. Dept. of Botany and Plant Pathology
  3. Oregon State Univ., Corvallis, OR (United States). Dept. of Electrical Engineering and Computer Science
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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 ~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. Availability: Implemented in C++, supersplat source code and binaries are freely available on the web at http://mocklerlabtools.cgrb.oregonstate.edu/
Research Organization:
Oregon State Univ., Corvallis, OR (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
FG02-08ER64630
OSTI ID:
1625268
Journal Information:
Bioinformatics, Journal Name: Bioinformatics Journal Issue: 12 Vol. 26; ISSN 1367-4803
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English

References (10)

Genome sequencing and analysis of the model grass Brachypodium distachyon journal February 2010
Next-generation DNA sequencing journal October 2008
RNA-Seq: a revolutionary tool for transcriptomics journal January 2009
A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome journal August 2008
Annotating genomes with massive-scale RNA sequencing journal January 2008
Applications of Ultra-high-Throughput Sequencing book January 2009
A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences journal June 2006
Optimal spliced alignments of short sequence reads journal August 2008
TopHat: discovering splice junctions with RNA-Seq journal March 2009
Genome-wide mapping of alternative splicing in Arabidopsis thaliana journal October 2009

Cited By (15)

The genome of woodland strawberry (Fragaria vesca) journal December 2010
CRCDA—Comprehensive resources for cancer NGS data analysis journal January 2015
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools journal December 2011
TrueSight: a new algorithm for splice junction detection using RNA-seq journal December 2012
Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length conference December 2010
PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text journal April 2012
Estimation of data-specific constitutive exons with RNA-Seq data journal January 2013
Genome-wide Profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays journal January 2012
Current status and future perspectives for sequencing livestock genomes journal March 2012
SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data journal January 2012
A Comparison of Single Molecule and Amplification Based Sequencing of Cancer Transcriptomes journal March 2011
GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences journal October 2011
A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq journal October 2011
SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data journal January 2011
Tools for mapping high-throughput sequencing data journal October 2012

Figures / Tables (6)

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