CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure.

ABSTRACT: With the exponential growth of sequence information stored over the last decade, including that of de novo assembled contigs from RNA-Seq experiments, quantification of chimeric sequences has become essential when assembling read data. In transcriptomics, de novo assembled chimeras can closely resemble underlying transcripts, but patterns such as those seen between co-evolving sites, or mapped read counts, become obscured. We have created a de Bruijn based de novo assembler for RNA-Seq data that utilizes a classification system to describe the complexity of underlying graphs from which contigs are created. Each contig is labelled with one of three levels, indicating whether or not ambiguous paths exist. A by-product of this is information on the range of complexity of the underlying gene f

SUBMITTER: Linheiro R 

PROVIDER: S-EPMC8651127 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature