STAR: ultrafast universal RNA-seq aligner

By Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark J. P. Chaisson, Thomas R. Gingeras. Bioinform., 2013

20,222 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/78ce0c149860363bbbe34306c75a4454ad23828d

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In Molecular Biology

Citations in the corpus

A survey of best practices for RNA-seq data analysis (2016, methodology): “Several other mappers exist that are optimized to identify SNPs or indels (GSNAP [202], PALMapper [203] MapSplice [204]), detect non-canonical splice junctions (STAR [15], MapSplice [204]), achieve ultra-fast mapping (GEM [205]) or map long-reads (STAR [15]).”
Mapping RNA‐seq Reads with STAR (2015, methodology): “The STAR (Dobin et al., 2013) software package enables highly accurate and ultra-fast alignment of RNA-seq reads to a reference genome.”
Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. (2017, positive): “1 genome using the STAR alignment software (Dobin et al., 2013) andmapped reads were processed through Cuffdiff (Trapnell et al.”
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment (2020, positive): “1bwas used for alignment against the Gencode v27 reference genome (Dobin et al., 2013).”
Single-Cell Profiling and SCOPE-Seq Reveal Lineage Dynamics of Adult Ventricular-Subventricular Zone Neurogenesis and NOTUM as a Key Regulator (2020, positive): “0 with parameters –sjdbOverhang 65–twopassMode Basic–outSAMtype BAM Unsorted (Dobin et al., 2013).”
Batch effects in single-cell RNA sequencing data are corrected by matching mutual nearest neighbours (2018, methodology): “2a [26] with default parameters, and assigned to Ensembl build 86 protein-coding genes using featureCounts version 1.”
Radiotherapy induces responses of lung cancer to CTLA-4 blockade (2018, positive): “The sequencing reads were cleaned by trimming adapter sequences and low-quality bases, and then aligned to the human reference genome (GRCh37) using STAR 50 .”
The single cell transcriptional landscape of mammalian organogenesis (2019, positive): “Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, or a chimeric reference genome of human hg19 and mouse mm10 for HEK293T and NIH/3T3 mixed nuclei, using STAR/v 2.5.2b 55 with default settings and gene annotations (GENCODE V19 for human; GENCODE VM11 for mouse).”
Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction (2018, positive): “Sequencing reads were aligned to the mouse transcriptome using STAR aligner 45 .”