Tuxedo protocols

Tuxedo computational protocol

Tuxedo specifications


Unique identifier OMICS_01415
Name Tuxedo
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
TopHat, Cufflink
Maintained Yes


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  • person_outline Cole Trapnell <>

Publication for Tuxedo

Tuxedo IN pipelines

PMCID: 5805368
PMID: 29377900
DOI: 10.1371/journal.pgen.1007183

[…] to our assembled contigs using quast [34, 68]. 79.3% bases of the reference genome could be aligned in the new assembly., using available mrna-seq datasets [34], transcripts were identified by the tuxedo suite. initial mapping with tophat was followed by transcript annotation with cufflinks [69]. transcript similarity was estimated using blast2go., total rna isolated via the trizol method […]

PMCID: 5311114
PMID: 28217743
DOI: 10.1128/mSphere.00038-17

[…] sequenced on an illumina hiseq 2500 instrument. high-throughput sequencing reads were aligned to transcripts from the y. lipolytica clib122 genome (72) using bowtie2 (73) and quantified using the tuxedo suite of tools (74). a summary of the results of the expression analysis is available in data set s1 in the supplemental material. gene ontology analysis was performed using funrich (75). […]

PMCID: 5326516
PMID: 28202685
DOI: 10.1098/rsbl.2016.0914

[…] sequences were obtained on an illumina nextseq 500, replicated across two flow cells, with within-sample replicates pooled for further analysis [15]. we performed rnaseq data analysis using the tuxedo protocol in the dna subway online platform [16] with quality control using fastx-toolkit (v. reads were mapped to the d. melanogaster transcriptome and genome (ensembl r76, bdpg5) […]

PMCID: 5354443
PMID: 28264028
DOI: 10.1371/journal.ppat.1006266

[…] using illumina’s bcl2fastq v2.17.1.14 software. mapping rna-seq reads on the human genome (grch38) after trimming the adaptors, transcript assembly, and abundance estimation were performed using tuxedo suite pipeline (tophat v2.0.9/cufflinks v2.2.1) [72,73] and reported using fragments per kilobase of exon per million fragments mapped (fpkm). cuffdiff was used to calculate statistically […]

PMCID: 5404846
PMID: 28441405
DOI: 10.1371/journal.pone.0176022

[…] 23 million raw rnaseq reads per sample. fastq files are available at the ncbi sequence read archive (sra) under study number srp092151. differential expression analysis was performed using the tuxedo analysis suite [34]. briefly, bowtie2 along with tophat were used to align generated reads to the tair10 a. thaliana reference genome. after expressed transfrags were assembled, cufflinks […]

Tuxedo institution(s)
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Department of Computer Science, University of California, Berkeley, CA, USA; Computer Science and Artificial Intelligence Lab, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Department of Mathematics, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
Tuxedo funding source(s)
Supported by Director's New Innovator Awards (1DP2OD00667-01) and the Center of Excellence in Genome Science from the US National Human Genome Research Institute.

Tuxedo review

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Gyan Prakash Mishra

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This pipeline is deprecated now that is based in cufflinks. The newer version is HISAT-StringTie- Ballgown