SOLiD DNA sequences are typically analyzed using a reference genome, while they are not recommended for de novo assembly of genomes or transcriptomes. This is mainly due to the difficulty in translating the SOLiD color-space data into normal base-space sequences. In fact, the nature of color-space is such that any misinterpreted color leads to a chain of further translation errors, producing totally wrong results. Here we describe SATRAP, 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 at http://satrap.cribi.unipd.it, either as a multi-step pipeline incorporating several tools for RNA-seq assembly or as an individual module for use with the Oases package.

SATRAP: SOLiD assembler translation program / Campagna, Davide; Gasparini, Fabio; Franchi, Nicola; Manni, Lucia; Telatin, Andrea; Vitulo, Nicola; Ballarin, Loriano; Valle, Giorgio. - In: PLOS ONE. - ISSN 1932-6203. - 10:9(2015), pp. 1-7. [10.1371/journal.pone.0137436]

SATRAP: SOLiD assembler translation program

FRANCHI, NICOLA;
2015

Abstract

SOLiD DNA sequences are typically analyzed using a reference genome, while they are not recommended for de novo assembly of genomes or transcriptomes. This is mainly due to the difficulty in translating the SOLiD color-space data into normal base-space sequences. In fact, the nature of color-space is such that any misinterpreted color leads to a chain of further translation errors, producing totally wrong results. Here we describe SATRAP, 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 at http://satrap.cribi.unipd.it, either as a multi-step pipeline incorporating several tools for RNA-seq assembly or as an individual module for use with the Oases package.
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SATRAP: SOLiD assembler translation program / Campagna, Davide; Gasparini, Fabio; Franchi, Nicola; Manni, Lucia; Telatin, Andrea; Vitulo, Nicola; Ballarin, Loriano; Valle, Giorgio. - In: PLOS ONE. - ISSN 1932-6203. - 10:9(2015), pp. 1-7. [10.1371/journal.pone.0137436]
Campagna, Davide; Gasparini, Fabio; Franchi, Nicola; Manni, Lucia; Telatin, Andrea; Vitulo, Nicola; Ballarin, Loriano; Valle, Giorgio
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11380/1252943
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