Cufflinks

Application data
Created by	Cole Trapnell
Biological application domain(s)	RNA-Seq alignment, RNA-Seq quantification, Alternative splicing, Transcriptomics, RNA-Seq
Principal bioinformatics method(s)	Transcriptome assembly, Read mapping, Differential expression analysis, Differential expression analysis
Technology	Illumina, 454, Ion Torrent, Illumina HiSeq, Illumina Solexa
Created at	University of Maryland, UC Berkeley, Johns Hopkins University, Harvard University
Maintained?	Yes
Input format(s)	SAM
Output format(s)	GTF
Licence	Boost
Contact:	tophat.cufflinks@gmail.com

Summary: Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

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Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.

The Cufflinks home page is http://cufflinks.cbcb.umd.edu/.