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Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes

Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes

High-throughput RNA sequencing (RNA-seq) provides a comprehensive picture of the transcriptome, including the identity, structure, quantity, and variability of expressed transcripts in cells, through the assembly of sequenced short RNA-seq reads. Although the reference-based approach guarantees the high quality of ...

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Shannon – An Information-Optimal de Novo RNA-Seq Assembler

Shannon – An Information-Optimal de Novo RNA-Seq Assembler

De novo assembly of short RNA-Seq reads into transcripts is challenging due to sequence similarities in transcriptomes arising from gene duplications and alternative splicing of transcripts. A team led by researchers at the University of Washington have developed Shannon, an ...

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FRAMA – from RNA-seq data to annotated mRNA assemblies

FRAMA – from RNA-seq data to annotated mRNA assemblies

Advances in second-generation sequencing of RNA made a near-complete characterization of transcriptomes affordable. However, the reconstruction of full-length mRNAs via de novo RNA-seq assembly is still difficult due to the complexity of eukaryote transcriptomes with highly similar paralogs and multiple ...

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SATRAP – SOLiD Assembler TRAnslation Program

SATRAP – SOLiD Assembler TRAnslation Program

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. ...

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