A tool to assemble RNA-seq sequence alignments into transcripts. The StringTie algorithm can optionally make de novo assemblies and uses a novel network flow algorithm.
Transcriptomics; RNA-seq
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL "StringTie enables improved reconstruction of a transcriptome from RNA-seq reads." Nat Biotechnol. 2015 Mar;33(3):290-5. https://doi.org/10.1038/nbt.3122
PMID: 25690850
PMCID: PMC4643835
Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL "Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown." Nat Protoc. 2016 Sep;11(9):1650-67. https://doi.org/10.1038/nprot.2016.095
PMID: 27560171
PMCID: PMC5032908
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