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chevron_left Read quality control Normalization Known transcript quantification Differential expression De novo transcriptome assembly Bioinformatics workflows Novel transcript quantification Adapter trimming Transcriptome annotation chevron_right
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TRUFA specifications


Unique identifier OMICS_15052
Alternative name TRanscriptome User-Friendly Analysis
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Input format FASTQ, FASTA, HMM
Programming languages Javascript, Python, Shell (Bash)
Computer skills Basic
Stability Stable
Maintained Yes



  • person_outline Etienne Kornobis

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Publication for TRanscriptome User-Friendly Analysis

TRUFA citations


Phylogenetic relationships of cone snails endemic to Cabo Verde based on mitochondrial genomes

BMC Evol Biol
PMCID: 5702168
PMID: 29178825
DOI: 10.1186/s12862-017-1069-x
call_split See protocol

[…] The reads corresponding to each mt genome were sorted using the corresponding library indices, and read assembly was performed in the TRUFA webserver []. Briefly, adapters were removed using SeqPrep [], quality of the reads was checked using FastQC v.0.10.1 [], and raw sequences were trimmed and filtered out according to their quali […]


Next generation sequencing of representational difference analysis products for identification of genes involved in diosgenin biosynthesis in fenugreek (Trigonella foenum graecum)

PMCID: 5393294
PMID: 28161815
DOI: 10.1007/s00425-017-2657-0

[…] Bioinformatic analysis of raw reads was performed using Transcriptome User-Friendly Analysis (TRUFA; Kornobis et al. ), a webserver platform dedicated to RNA-seq analysis. A complete pipeline performs particular tasks in which read files are cleaned and th […]


A practical guide to build de novo assemblies for single tissues of non model organisms: the example of a Neotropical frog

PMCID: 5582611
PMID: 28879061
DOI: 10.7717/peerj.3702

[…] a de-novo transcriptome are now available, yet contrasting opinions about the steps to follow may be disorienting. Some extremely simple pipelines have been developed to automatize the process (e.g., TRUFA; ), but this may limit the flexibility of the different pieces of software that have been integrated.Here, we present the transcriptome profile for Oreobates cruralis, a direct-developing frog s […]


Deep, multi stage transcriptome of the schistosomiasis vector Biomphalaria glabrata provides platform for understanding molluscan disease related pathways

BMC Infect Dis
PMCID: 5084317
PMID: 27793108
DOI: 10.1186/s12879-016-1944-x

[…] mbly, contigs less than 500 bp in length were removed from our dataset, and final assembly metrics were determined using a perl script available from the authors upon request. CEGMA [] was run on the TRUFA platform []. […]


Merging scleractinian genera: the overwhelming genetic similarity between solitary Desmophyllum and colonial Lophelia

BMC Evol Biol
PMCID: 4870751
PMID: 27193263
DOI: 10.1186/s12862-016-0654-8

[…] e analyses using microsatellite sequences were performed. A total of 37 loci, previously characterized for L. pertusa [, ] and published in GenBank, were used to perform multiple BLAST searches using TRUFA 0.8.2 [], against D. dianthus genomic DNA libraries that were previously obtained by Illumina (data not shown) and 454 [] sequencing. This analysis of microsatellite sequences showed that averag […]


Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes

Front Genet
PMCID: 4707302
PMID: 26793234
DOI: 10.3389/fgene.2015.00361

[…] nge of eukaryotic species, thus providing a percentage “completeness” score (e.g., Chauhan et al., ; Moreton et al., ; Frías-López et al., ; Powell et al., ; Price et al., ). A recent web-based tool “TRUFA,” developed by Kornobis et al. (), incorporates CEGMA into its pipeline as part of the assessment stage of de novo assemblies. As of May 2015 CEGMA is no longer being supported, however a new to […]

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TRUFA institution(s)
Departamento de biodiversidad y biología evolutiva, Museo Nacional de Ciencias Naturales MNCN (CSIC), Madrid, Spain; Instituto de Física de Cantabria, IFCA (CSIC-UC), Edificio Juan Jordá, Santander, Spain; Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
TRUFA funding source(s)
This work was partially funded with Spanish Ministry of Science and Innovation grants CGL2010–18216 and CGL2013–45211-C2–2-P and CGL2013–45211-C2–1-P; by ICREA Academia (Generalitat de Catalunya; Spain).

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