Transcriptome Assembly Tools

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De novo assembly of bacterial transcriptomes from RNA-seq data

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

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

Enabling large-scale next-generation sequence assembly with Blacklight

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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A comparison of De novo short read sequence assemblers

A comparison of De novo short read sequence assemblers

The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, ...

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