De novo assembly of bacterial transcriptomes from RNA-seq data.
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ABSTRACT:
SUBMITTER: Tjaden B
PROVIDER: S-EPMC4316799 | biostudies-literature | 2015 Jan
REPOSITORIES: biostudies-literature
Publications
De novo assembly of bacterial transcriptomes from RNA-seq data.
Genome biology 20150113
Transcriptome assays are increasingly being performed by high-throughput RNA sequencing (RNA-seq). For organisms whose genomes have not been sequenced and annotated, transcriptomes must be assembled de novo from the RNA-seq data. Here, we present novel algorithms, specific to bacterial gene structures and transcriptomes, for analysis of bacterial RNA-seq data and de novo transcriptome assembly. The algorithms are implemented in an open source software system called Rockhopper 2. We find that Roc ...[more]
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| S-EPMC3485621 | biostudies-literature
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| S-EPMC3287467 | biostudies-literature
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Project description:Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise. Here, we present TRAPID, an online tool for the fast and efficient processing of assembled RNA-Seq transcriptome data, developed to mitigate these challenges. TRAPID offers high-throughput open reading frame detection, frameshift correction and includes a functional, comparative and phylogenetic toolbox, making use of 175 reference proteomes. Benchmarking and comparison against state-of-the-art transcript analysis tools reveals the efficiency and unique features of the TRAPID system. TRAPID is freely available at http://bioinformatics.psb.ugent.be/webtools/trapid/.
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