Details

Autor(en) / Beteiligte

• Campagna, Davide
• Gasparini, Fabio
• Franchi, Nicola
• Manni, Lucia
• Telatin, Andrea
• Vitulo, Nicola
• Ballarin, Loriano
• Valle, Giorgio
• Jordan, I. King

Titel

SATRAP: SOLiD Assembler TRAnslation Program

Ist Teil von

• PloS one, 2015-09, Vol.10 (9), p.e0137436-e0137436

Ort / Verlag

United States: Public Library of Science

Erscheinungsjahr

2015

Link zum Volltext

Quelle

MEDLINE

Beschreibungen/Notizen

• 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.