TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms

• DOI: 10.1186/s12859-018-2384-y
• Publication Date: 2018-11-16T15:30:51Z
• Authors: Pedro Seoane; Marina Espigares; Rosario Carmona; Álvaro Polonio; Julia Quintana; Enrico Cretazzo; Josefina Bota; Alejandro Pérez-G...; Juan de Dios Alché; Luis Gómez; M. Gonzalo Claros
• Keywords: Sequence assembly

The advances in high-throughput sequencing technologies are allowing more and de novo assembling of transcriptomes from many new organisms. Some degree automation evaluation is required to warrant reproducibility, repetitivity the selection best possible transcriptome. Workflows pipelines becoming an absolute requirement for such a purpose, but issue organisms lacking sequenced genome remains unsolved. An automated, reproducible flexible framework called TransFlow accomplish this task described. with its five independent modules was designed build different workflows depending on nature original reads. This architecture enables combinations Illumina Roche/454 data, can be extended other platforms. Its capabilities illustrated reliable plant reference six (three case studies grapevine leaves, olive tree pollen, chestnut stem, three haustorium, epiphytic structures their combination phytopathogenic fungus Podosphaera xanthii). Arabidopsis poplar revealed references. A common result regarding assemblies that paired-end reads 100 nt length assembled OASES provide transcriptomes, while contribution longer noticeable only when they complement set short, single-reads. handle up 181 strategies. Evaluation based principal component analyses allows self-adaptation sets suitable transcriptome each assemblers. As result, study has own behaviour, prioritises parameters, gives objective automated way detecting within pool them. Sequencing data type quantity (preferably several hundred millions 2×100 or longer), assemblers (OASES Illumina, MIRA4 EULER-SR reconciled CAP3 Roche/454) strategy scaffolding OASES, probably merging available) arise as most impacting factors.