It mapped more than 2.2 million reads per CPU hour. When TopHat first came out, it was faster than previous systems. TopHat can be used with the Tuxedo pipeline, and is frequently used with Bowtie.Īdvantages/Disadvantages Advantages It is useful because it does not need to rely on known splice sites. It is a read-mapping algorithm and it aligns the reads to a reference genome. TopHat is used to align reads from an RNA-Seq experiment. TopHat is a collaborative effort between Cole Trapnell at the University of Washington and Daehwan Kim and Steven Salzberg in the Center for Computational Biology at Johns Hopkins University who together in 2013 also came up with TopHat2 which does accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Trapnell later moved to Genome Sciences Department at the University of Washington. ![]() TopHat was originally developed in 2009 by Cole Trapnell, Lior Pachter and Steven Salzberg at the Mathematics Department, UC Berkeley and the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park.
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