STAR
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Application data |
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| Created by | Alexander Dobin |
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| Biological application domain(s) | RNA-seq, Transcriptomics |
| Principal bioinformatics method(s) | Sequence alignment |
| Technology | Illumina, 454, Sanger, Ion Torrent, PacBio |
| Created at | CSHL |
| Maintained? | Yes |
| Input format(s) | FASTA, FASTQ |
| Output format(s) | SAM |
| Programming language(s) | C++ |
| Licence | GPLv3 |
| Operating system(s) | Linux, Unix, Mac OS X; x86_64 |
Summary: Ultrafast universal RNA-seq aligner
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Description
MOTIVATION: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases.
RESULTS: To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy.
AVAILABILITY AND IMPLEMENTATION: STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license.
Links
References
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