STAR specifications

Information


Unique identifier OMICS_01254
Name STAR
Alternative name Spliced Transcripts Alignment to a Reference
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.5.4b
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Alexander Dobin <>

STAR article

STAR citations

 (3)
2017
PMCID: 5758914

[…] were prepared with the rrna depletion protocol and sequenced on an illumina hiseq2500 with a read length of 50 bases. quality check was performed using tool fastqc. reads were aligned with star (spliced transcripts alignment to a reference) to release 86 of the mus musculus ensembl version of the genome (grmm38/mm10 assembly). htseq-count tool from htseq package was used to count the number […]

2016
PMCID: 4997733

[…] an initial human-sequence removal step is accomplished by alignment of all paired-end reads to the human reference genome 38 (hg38) and the pan troglodytes genome (pantro4, 2011, ucsc), using the spliced transcripts alignment to a reference (star) aligner (v2.5.1b) [10]. unaligned reads were quality filtered using priceseqfilter [11] with the “-rnf 90” and “-rqf 85 0.98” settings. reads […]

2015
PMCID: 4444957

[…] on quality (phred quality score ≥20) and size (read length ≥21 bp), in order to enrich for high quality reads corresponding to pirnas. samples were realigned to human genome (hg19) using the the spliced transcripts alignment to a reference (star) software, with one mismatch was allowed during re-mapping of sequence reads to the human genome61 and a custom pirna reference transcriptome using […]

STAR institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Pacific Biosciences, Menlo Park, CA, USA
STAR funding source(s)
Supported by NHGRI (NIH) grant U54HG004557.

STAR reviews

 (2)
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Antoine Rousselin

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Desktop
Common use in targeted RNA-seq.

Very rich tool, still a lot of parameters to use and understand!
Claudia Armenise Quartz Bio's avatar image No country

Claudia Armenise Quartz Bio

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Desktop
A very fast mapping tool. Cons: requires a lot of RAM, cannot perform quality-depend mapping whereas Bowtie offers this option