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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

Information


Unique identifier OMICS_15052
Name TRUFA
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

Documentation


Maintainer


  • person_outline Etienne Kornobis <>

Additional information


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Publication for TRanscriptome User-Friendly Analysis

TRUFA in publications

 (7)
PMCID: 5702168
PMID: 29178825
DOI: 10.1186/s12862-017-1069-x

[…] 2 × 150 paired-end) at sistemas genómicos (valencia, spain)., 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 […]

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

[…] nextera xt dna library preparation guide. cdna libraries were sequenced using paired end illumina miseq. raw data were saved in fastq format., 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 […]

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

[…] 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 [].table 1 , we searched for homologues and annotated our dataset according to go terms with blast2go 2.5.0 (web start) queries against the nr database [, ]. d. melanogaster go term […]

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

[…] 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 […]


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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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