Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• *De novo* transcriptome assembly from short reads is crucial for organisms without reference genomes.
• Existing assemblers like Trinity and Oases provide good quality contigs but can be improved for compaction and error correction.
• Transcriptome assembly quality metrics include chimera and nucleotide error rates, alongside contig count.

Purpose of the Study:

• To develop a pipeline that enhances the results of *de novo* transcriptome assemblers.
• To improve the compaction and quality of assembled transcriptomes.
• To provide an easy-to-use, open-source software for RNA-Seq assembly.

Main Methods:

• Development of the De Novo RNA-Seq Assembly Pipeline (DRAP).
• DRAP integrates and wraps existing assemblers such as Trinity and Oases.
• Comparative analysis of assembly results with and without DRAP.

Main Results:

• DRAP reduces the number of contigs by 1.3 to 15-fold compared to standalone assemblers.
• The pipeline improves assembly compaction and quality without significantly impairing key metrics like read realignment rate.
• Assembly comparisons demonstrated substantial improvements using DRAP.

Conclusions:

• *De novo* transcriptome assembly can be computationally challenging but offers room for improvement.
• The De Novo RNA-Seq Assembly Pipeline (DRAP) provides a user-friendly solution for generating compact and corrected transcript sets.
• DRAP is freely available as open-source software, facilitating its adoption in research.