GTax – improving de novo transcriptome assembly by removing foreign RNA contamination

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The cost and complexity of generating a complete reference genome means that many organisms lack an annotated reference. An alternative is to use a de novo reference transcriptome. This technology is cost-effective but is susceptible to off-target RNA contamination. Researchers at the National Center for Biotechnology Information have developed GTax, a taxonomy-structured database of genomic sequences that can be used with BLAST to detect and remove foreign contamination in RNA sequencing samples before assembly. In addition, the researchers use a de novo transcriptome assembly of Solanum lycopersicum (tomato) to demonstrate that removing foreign contamination in sequencing samples reduces the number of assembled chimeric transcripts.

Fig. 1

Workflow to remove vectors and contaminated transcripts after assembly completion. Different levels of decontamination of the SRA samples were used to assemble three transcriptomes: Trimmed, Eudicotyledons, and Eudicotyledons + unidentified

Availability – GTax is implemented as a Python package under Public Domain license. Source code is available at

Alvarez RV, Landsman D. (2024) GTax: improving de novo transcriptome assembly by removing foreign RNA contamination. Genome Biol 25(1):12. [article]