TopHat statistics

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TopHat specifications


Unique identifier OMICS_01257
Name TopHat
Alternative name TopHat2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++, Python
Computer skills Advanced
Version 2.1.1
Stability Stable
Bowtie, Bowtie-align, Bowtie-inspect, Bowtie-build, samtools
Maintained Yes



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  • person_outline Cole Trapnell <>

Publications for TopHat

TopHat in pipelines

PMCID: 5743717
PMID: 29290775
DOI: 10.7150/jca.21925

[…] and chip-seq data shared the same experimental condition—hela cells were treated with egf (100 ng/ml) for 20 min after 48 hr serum starvation. rna-seq data was aligned to the human genome hg19 using tophat. unmapped reads were filtered out. transcripts were assembled by cufflink. differential expression of transcripts was estimated by cuffdiff . for chip-seq data, bowtie2 was used for mapping […]

PMCID: 5751775
PMID: 29298675
DOI: 10.1186/s12870-017-1218-9

[…] ca, usa). low-quality nucleotides (<q15) from both the 5′- and the 3′-ends were trimmed by using btrim []. reads were aligned to the reference genome of btx623 (sbicolor_v1.4_79) [] by using tophat version 2.0.4 []. differentially expressed genes were identified by using cuffdiff version 2.2.0 [], with the gene models annotated in sbicolor ver1.4 []., mapman (3.5.1 r2) software [] […]

PMCID: 5753478
PMID: 29298683
DOI: 10.1186/s12864-017-4386-y

[…] gviz package []. density plots were generated with the lsd package (, linear rna-seq reads were mapped to the c. elegans ce11 annotation using tophat [] with default settings. to quantify the differential expression across time-points, we used cuffdiff []. genes with fold changes > 1.5 and a benjamini-hochberg corrected p value < 0.05 […]

PMCID: 5754085
PMID: 29300744
DOI: 10.1371/journal.pone.0189185

[…] sequences, empty reads, low-quality sequences, and short reads. the high-quality reads were aligned to the phaseolus vulgaris genome (v1.0), available in phytozome (joint genome institute), using tophat2/bowtie2 [, ]. reads overlapping with the annotation range of interest were counted for each sample using the “summarizeoverlaps” function []. read counting was performed for exonic gene […]

PMCID: 5755174
PMID: 29301509
DOI: 10.1186/s12885-017-3945-6

[…] from and normalized to actb expression. publicly available rna-seq libraries for fetal testis (additional file : table s9) were filtered with fastx-toolkit and a conventional tophat v2.0.9/cufflinks v2.1.1 pipeline with default parameters and reference annotation from ensembl release 83 was employed [–]., cell line tera1 (atcc htb-105) was purchased from attc (usa) […]

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TopHat in publications

PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] reads in the mayo clinic medical genomics core. gene expression profiles were obtained using the map-rseq v.1.2.1 workflow, the mayo bioinformatics core pipeline. map-rseq consists of alignment with tophat 2.0.6 against the human hg19 genome build and gene counts with the htseq software 0.5.3p9 ( using gene annotation files obtained […]

PMCID: 5958096
PMID: 29773799
DOI: 10.1038/s41467-018-04398-z

[…] read qualities in those bases as compared to the remainder of the read. trimmed reads that passed the trimmomatic selection criteria were then aligned to the rn6 build of the rat genome with bowtie2/tophat2, using default parameters. aligned reads were assigned to gene-level genomic features of the ensembl 83 annotation set using the rsubread featurecounts r function with countmultimappingreads […]

PMCID: 5958101
PMID: 29773797
DOI: 10.1038/s41467-018-04364-9

[…] conditions (supplementary table ). total rna was collected from fermentations of s. schorii grown in aspm (production) and dpy (non-production) media and sequenced by standard illumina methods. tophat2 was used to map quality-filtered reads onto the s. schorii draft genome. differential gene expression was then analysed with readxplorer 2.0 including the deseq package. the results (fig. ) […]

PMCID: 5956100
PMID: 29769607
DOI: 10.1038/s41598-018-25998-1

[…] base calling, and read-quality filtering were done using the casava pipeline version 1.8.2 (illumina). each sample was processed and analyzed with the same methods. after filtering low quality reads tophat version 2.1.0 was used to align all reads to the mm10 genome with default parameters and to identify splice junctions,. htseq was used to create count tables from tophat2 aligned reads. deseq2 […]

PMCID: 5955945
PMID: 29769567
DOI: 10.1038/s41598-018-25800-2

[…] the 100 bp paired-end mode of the truseq rapid pe cluster kit and truseq rapid sbs kit (illumina, usa)., the reads from the fastq files were mapped against the hg19 human reference genome using tophat version 2.0.6 ( raw read counts mapped onto genes were measured with the bam format file by htseq version 0.6.1. then a total of 18,161 coding genes were subjected […]

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TopHat institution(s)
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Department of Computer Science, University of Maryland, College Park, MD, USA; Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, USA; Illumina Inc., San Diego, CA, USA
TopHat funding source(s)
This work is supported in part by the National Human Genome Research Institute (NIH) under grants R01-HG006102 and R01-HG006677.

TopHat reviews

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Arup Ghosh

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A popular tool for RNA-seq alignment but major disadvantages are slow and support discontinued after the launch of HISAT.
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Anonymous user #60

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Useful tool to map mRNA-seq reads, i.e. to align reads mapping onto multiple exons. Unfortunately, the support team is not very reactive to fix bugs.