Transcriptome Assembly Tools

De novo assembly of bacterial transcriptomes from RNA-seq data

A number of mature computational tools exist for both reference-based transcriptome assembly and de novo transcriptome assembly. However, most of the aforementioned tools were designed primarily for eukaryotic transcriptomes. Bacterial transcriptome assembly faces different challenges than eukaryotic transcriptome assembly. For ...

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Bayesembler – bayesian transcriptome assembly

RNA-seq allows for simultaneous transcript discovery and quantification, but reconstructing complete transcripts from such data remains difficult. Here, researchers from the University of Copenhagen introduce the Bayesembler, a novel probabilistic method for transcriptome assembly built on a Bayesian model of ...

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Enabling large-scale next-generation sequence assembly with Blacklight

rna-seq

A variety of extremely challenging biological sequence analyses were conducted on the XSEDE large shared memory resource Blacklight, using current bioinformatics tools and encompassing a wide range of scientific applications. These include genomic sequence assembly, very large metagenomic sequence assembly, ...

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Astroid – transcriptome reconstruction on the basis of a flow network

rna-seq

The advancement of RNA sequencing (RNA-seq) has provided an unprecedented opportunity to assess both the diversity and quantity of transcript isoforms in an mRNA transcriptome. In this paper, researchers from the University of Kentucky revisit the computational problem of transcript ...

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