Cufflinks | Tool name | Cufflinks |
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| URL | http://cufflinks.cbcb.umd.edu/ |
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| Important features | 1. It 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.
2. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.
3. Cufflinks implements a constructive proof of Dilworth's Theorem by constructing a covering relation on the read alignments, and finding a minimum path cover on the directed acyclic graph for the relation. Works well with unpaired RNA-Seq reads. |
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| Citations | Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5. Epub 2010 May 2. PubMed PMID: 20436464. |
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| Year of publication | 2010 |
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| Rank by usage frequency | 100 |
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| Comments | Requires installation of Boost C++ libraries and SAMtools. |
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| Function | RNA seq alignment, Transcriptome assembler, RNA seq analysis |
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| Category | Free, Downloadable |
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| License | Boost |
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| Status | |
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| Input file format | SAM, BAM |
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| Output file format | GTF |
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| Operating system | Mac OS X,Linux |
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| Maintained by | NCBI-NLM |
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