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A computer program designed to efficiently translate de novo assembled color-space sequences into a base-space format. The program was tested and validated using simulated and real transcriptomic data; its modularity allows an easy integration into more complex pipelines, such as Oases for RNA-seq de novo assembly. SATRAP is available either as a multi-step pipeline incorporating several tools for RNA-seq assembly or as an individual module for use with the Oases package.

Software type:
Command line interface
Restrictions to use:
Biological technology:
Life Technologies
Operating system:
Programming languages:
Computer skills:
SATRAP version 0.1
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  • Davide Campagna <satrap at cribi.unipd.it>


CRIBI Biotechnology Centre, Università di Padova, Padova, Italy; Department of Biology, Università di Padova, Padova, Italy

Funding source(s)

This work was funded by Università degli Studi di Padova, Progetto Strategico 2011 BIOINFOGEN; Consiglio Nazionale delle Ricerche, Progetto EPIGEN; and Fondazione Cassa di Risparmio di Padova e Rovigo, Progetti di eccellenza 2008.

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    PMID: 21559467
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    PMID: 22676195
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    PMID: 24086547
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    PMID: 23358380
  • (Bradnam et al., 2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience.
    PMID: 23870653
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    PMID: 22147368
  • (Utturkar et al., 2014) Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. Bioinformatics.
    PMID: 24930142
  • (Alkan et al., 2011) Limitations of next-generation genome sequence assembly. Nature methods.
    PMID: 21102452
  • (Love et al., 2016) Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly. BMC genomics.
    PMID: 26944054

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