title: SATRAP: SOLiD Assembler TRAnslation Program.
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.
authors.affiliation: CRIBI Biotechnology Centre, Università di Padova, Padova, Italy; Department of Biology, Università di Padova, Padova, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Campagna
authors.affiliation: Department of Biology, Università di Padova, Padova, Italy.
authors.forename: Fabio
authors.initials: F
authors.lastname: Gasparini
authors.affiliation: Department of Biology, Università di Padova, Padova, Italy.
authors.forename: Nicola
authors.initials: N
authors.lastname: Franchi
authors.affiliation: Department of Biology, Università di Padova, Padova, Italy.
authors.forename: Lucia
authors.initials: L
authors.lastname: Manni
authors.affiliation: CRIBI Biotechnology Centre, Università di Padova, Padova, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Telatin
authors.affiliation: Department of Biology, Università di Padova, Padova, Italy.
authors.forename: Nicola
authors.initials: N
authors.lastname: Vitulo
authors.affiliation: Department of Biology, Università di Padova, Padova, Italy.
authors.forename: Loriano
authors.initials: L
authors.lastname: Ballarin
authors.affiliation: CRIBI Biotechnology Centre, Università di Padova, Padova, Italy; Department of Biology, Università di Padova, Padova, Italy.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Valle
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome