Tools for building de novo transcriptome assembly
نویسندگان
چکیده
منابع مشابه
Clustering of Short Read Sequences for de novo Transcriptome Assembly
Given the importance of transcriptome analysis in various biological studies and considering thevast amount of whole transcriptome sequencing data, it seems necessary to develop analgorithm to assemble transcriptome data. In this study we propose an algorithm fortranscriptome assembly in the absence of a reference genome. First, the contiguous sequencesare generated using de Bruijn graph with d...
متن کاملclustering of short read sequences for de novo transcriptome assembly
given the importance of transcriptome analysis in various biological studies and considering thevast amount of whole transcriptome sequencing data, it seems necessary to develop analgorithm to assemble transcriptome data. in this study we propose an algorithm fortranscriptome assembly in the absence of a reference genome. first, the contiguous sequencesare generated using de bruijn graph with d...
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MOTIVATION Whole transcriptome shotgun sequencing data from non-normalized samples offer unique opportunities to study the metabolic states of organisms. One can deduce gene expression levels using sequence coverage as a surrogate, identify coding changes or discover novel isoforms or transcripts. Especially for discovery of novel events, de novo assembly of transcriptomes is desirable. RESUL...
متن کاملInformed kmer selection for de novo transcriptome assembly
MOTIVATION De novo transcriptome assembly is an integral part for many RNA-seq workflows. Common applications include sequencing of non-model organisms, cancer or meta transcriptomes. Most de novo transcriptome assemblers use the de Bruijn graph (DBG) as the underlying data structure. The quality of the assemblies produced by such assemblers is highly influenced by the exact word length k As su...
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Researchers interested in studying and constructing transcriptomes, especially for non-model species, face the conundrum of choosing from a number of available de novo and genome-guided assemblers. None of the popular assembly tools in use today achieve requisite sensitivity, specificity or recovery of full-length transcripts on their own. Here, we present a comprehensive comparative study of t...
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ژورنال
عنوان ژورنال: Current Plant Biology
سال: 2017
ISSN: 2214-6628
DOI: 10.1016/j.cpb.2017.12.004