Pincho: A Modular Approach to High Quality De Novo Transcriptomics.

ABSTRACT: Transcriptomic reconstructions without reference (i.e., de novo) are common for data samples derived from non-model biological systems. These assemblies involve massive parallel short read sequence reconstructions from experiments, but they usually employ ad-hoc bioinformatic workflows that exhibit limited standardization and customization. The increasing number of transcriptome assembly software continues to provide little room for standardization which is exacerbated by the lack of studies on modularity that compare the effects of assembler synergy. We developed a customizable management workflow for de novo transcriptomics that includes modular units for short read cleaning, assembly, validation, annotation, and expression analysis by connecting twenty-five individual bioinformatic tool

SUBMITTER: Ortiz R 

PROVIDER: S-EPMC8304035 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature