STAR (bioinformatics)
| Developer(s) | Alex Dobin |
|---|---|
| Stable release | 2.7.4a
/ 30 May 2020 |
| Written in | C++ |
| Engine | |
| Operating system | OS X, Linux |
| Type | Bioinformatics tool |
| License | MIT License |
| Website | github |
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In bioinformatics, STAR (Spliced Transcripts Alignment to a Reference)[1] is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of RNA molecules to reference genomes.
Such sequence alignment tools are used for single-cell transcriptomics to measure the gene expression of single biological cells. It is a de novo splice aligner that also uses annotation optionally, similar to TopHat (bioinformatics).
Cell Ranger, the set of pipelines provided 10x Genomics to analyse output from their single-cell RNA-sequencing machines uses STAR to align reads to a reference genome.[2]
Workflow[edit]
The standard STAR workflow consists of two steps[3]:
- Generating genome index files, and
- Mapping reads to the genome.
The aligned reads can either be in the SAM_(file_format) or its binary variant BAM. For novel splice junction discovery, a two-pass alignment option exists. Furthermore, the pipeline STARsolo is able to demultiplex sequencing data and so count gene reads from single-cell RNA-seq data.
Advantages/Disadvantages[edit]
STAR has large sensitivity and accuracy and is fast but has a high memory consumption.[4]
References[edit]
- ↑ Dobin, Alex (2013). "STAR: ultrafast universal RNA-seq aligner". Bioinformatics. 29 (1): 15–21. doi:10.1093/bioinformatics/bts635.
- ↑ "What is Cell Ranger". 10x Genomics. Retrieved 7 June 2020.
- ↑ Dobin, Alex. "STAR Manual" (PDF). Github. Retrieved 7 June 2020.
- ↑ "Best RNA-Seq aligner: A comparison of mapping tools". Retrieved 7 June 2020.
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