TopHat2

URI: https://gptkb.org/entity/TopHat2
GPTKB entity
Statements (33)
Predicate Object
gptkbp:instanceOf gptkb:software
gptkbp:basedOn gptkb:Bowtie2
gptkbp:citation >10,000
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36.
gptkbp:deprecatedIn yes
gptkbp:detects deletions
gene fusions
insertions
novel splice junctions
gptkbp:developedBy gptkb:Daehwan_Kim
gptkb:Steven_Salzberg
gptkbp:format gptkb:FASTQ
gptkb:SAM
BAM
junctions.bed
https://www.w3.org/2000/01/rdf-schema#label TopHat2
gptkbp:latestReleaseVersion 2.1.1
gptkbp:license open source
gptkbp:operatingSystem gptkb:Windows
gptkb:macOS
gptkb:Linux
gptkbp:releaseYear 2013
gptkbp:replacedBy gptkb:HISAT2
gptkb:TopHat
gptkbp:supports paired-end reads
single-end reads
gptkbp:usedFor RNA-Seq data analysis
splice junction mapping
gptkbp:website https://ccb.jhu.edu/software/tophat/index.shtml
gptkbp:writtenBy gptkb:Python
gptkb:C++
gptkbp:bfsParent gptkb:HISAT2
gptkbp:bfsLayer 7