Spliced Transcripts Alignment to a Reference (STAR)

Spliced Transcripts Alignment to a Reference (STAR) is a fast RNA-Seq read mapper, with support for splice-junction and fusion read detection.

STAR aligns reads by finding the Maximal Mappable Prefix (MMP) hits between reads (or read pairs) and the genome, using a Suffix Array index. Different parts of a read can be mapped to different genomic positions, corresponding to splicing or RNA-fusions. The genome index includes known splice-junctions from annotated gene models, allowing for sensitive detection of spliced reads. STAR performs local alignment, automatically soft clipping ends of reads with high mismatches.

For more information, see github.com/alexdobin/STAR.