TransPi – a comprehensive TRanscriptome ANalysiS PIpeline forde novotranscriptome assembly

Abstract

The use of RNA-Seq data and the generation of de novo transcriptome assemblies have been piv- otal for studies in ecology and evolution. This is distinctly true for non-model organisms, where no genome information is available; yet, studies of differential gene expression, DNA enrichment baits design, and phylogenetics can all be accomplished with the data gathered at the transcrip- tomic level. Multiple tools are available for transcriptome assembly, however, no single tool can provide the best assembly for all datasets. Therefore, a multi assembler approach, followed by a reduction step, is often sought to generate an improved representation of the assembly. To reduce errors in these complex analyses while at the same time attaining reproducibility and scalabil- ity, automated workflows have been essential in the analysis of RNA-Seq data. However, most of these tools are designed for species where genome data is used as reference for the assembly process, limiting their use in non-model organisms. We present TransPi, a comprehensive pipeline for de novo transcriptome assembly, with minimum user input but without losing the ability of a thorough analysis. A combination of different model organisms, kmer sets, read lengths, and read quantities were used for assessing the tool. Furthermore, a total of 49 non-model organisms, span- ning different phyla, were also analyzed. Compared to approaches using single assemblers only, TransPi produces higher BUSCO completeness percentages, and a concurrent significant reduction in duplication rates. TransPi is easy to configure and can be deployed seamlessly using Conda, Docker and Singularity.

Molecular and mineral responses of corals grown under artificial Calcite Sea conditions

“…Transcriptomes were assembled with TransPi (Rivera-Vicéns et al, 2022). Contigs of length < 300 bp were discarded.…”

Alphaflexivirus Genomes in Stony Coral Tissue Loss Disease-Affected, Disease-Exposed, and Disease-Unexposed Coral Colonies in the U.S. Virgin Islands

“…Noncoral/non-Symbiodiniaceae reads were combined and normalized using BBnorm.sh within BBMap ( Table 1 ). Normalized reads were assembled using the program TransPi ( 17 ). Multiple assemblies were generated using rnaSPADES v3.14.0 (kmer: 75,85,91,107 nucleotides) ( 18 ), Trans-ABySS v2.0.1 (kmer: 25,35,55,75,85 nucleotides) ( 19 ), SOAPdenovo-Trans v1.03 (kmer: 25,35,55,75,85 nucleotides) ( 20 ), Trinity v2.9.1 (kmer: 35 nucleotides) ( 11 ), and Velvet v1.2.12/Oases v0.2.09 (kmer: 65,71,81,87,91,97,101 nucleotides) ( 21 , 22 ).…”

Transcriptomic response of Cinachyrella cf. cavernosa sponges to spatial competition

“…For the generation of the de novo transcriptome assemblies the reads were processed using TransPi (Rivera-Vicéns, García-Escudero, Conci, Eitel, & Wörheide, 2021). Briefly, reads were assessed for quality, normalized, and assembled using a combination of different assemblers and different k-mer lengths.…”

“…cavernosa was created by combining all assemblies obtained from the reduction steps explained above and applying TransPi with a final reduction step. The annotation was also performed using TransPi (Rivera-Vicéns et al, 2021). It employed various databases such as SwissProt, PFAM, and a custom UniProt database (i.e., all metazoan proteins) to create a final report including information on gene ontology (GO), eggNOG, KEGG, PFAM, proteins similarities to SwissProt and UniProt, among others.…”