Compacta: a fast contig clustering tool for de novo assembled transcriptomes.

ABSTRACT:

Background

RNA-Seq is the preferred method to explore transcriptomes and to estimate differential gene expression. When an organism has a well-characterized and annotated genome, reads obtained from RNA-Seq experiments can be directly mapped to that genome to estimate the number of transcripts present and relative expression levels of these transcripts. However, for unknown genomes, de novo assembly of RNA-Seq reads must be performed to generate a set of contigs that represents the transcriptome. These contig sets contain multiple transcripts, including immature mRNAs, spliced transcripts and allele variants, as well as products of close paralogs or gene families that can be difficult to distinguish. Thus, tools are needed to select a set of less redundant contigs to represent the

SUBMITTER: Razo-Mendivil FG 

PROVIDER: S-EPMC7014741 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature