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STAR (bioinformatics)

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STAR
Developer(s)Alex Dobin
Stable release
2.7.4a / 30 May 2020; 4 years ago (2020-05-30)
Written inC++
Engine
    Operating systemOS X, Linux
    TypeBioinformatics tool
    LicenseMIT License
    Websitegithub.com/alexdobin/STAR

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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]:

    1. Generating genome index files, and
    2. 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]

    1. Dobin, Alex (2013). "STAR: ultrafast universal RNA-seq aligner". Bioinformatics. 29 (1): 15–21. doi:10.1093/bioinformatics/bts635.
    2. "What is Cell Ranger". 10x Genomics. Retrieved 7 June 2020.
    3. Dobin, Alex. "STAR Manual" (PDF). Github. Retrieved 7 June 2020.
    4. "Best RNA-Seq aligner: A comparison of mapping tools". Retrieved 7 June 2020.


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