Bellerophon

Bellerophon is a software pipeline that assesses and improves the quality of de novo assembled transcriptomes by focusing on removing chimeric sequences. Chimeric sequences can arise from faulty assembly, merging two transcripts into one. Assessing the quality of de novo assembled transcriptomes is challenging due to the absence of a reference genome for comparison.

The Bellerophon pipeline incorporates several steps to address this issue:
It uses TransRate, a quality assessment tool, to evaluate the initial quality of the transcriptome.
It applies a transcripts per million (TPM) filter to remove contigs with low expression levels.
It employs CD-HIT-EST to eliminate highly identical contigs.

To validate the effectiveness of Bellerophon, three benchmark experiments were conducted:
Computationally creating chimeras
Identifying chimeric contigs in a transcriptome assembly
Simulating an RNA-Seq experiment using a known reference transcriptome

The results showed that Bellerophon successfully removed between 40% and 91.9% of the chimeras in the transcriptome assemblies, with a higher removal rate for chimeric contigs than nonchimeric ones.