To assemble or not to resemble—A validated Comparative Metatranscriptomics Workflow (CoMW)

• Published in: GigaScience
• Main Authors: Muhammad Zohaib Anwar, Anders Lanzen, Toke Bang-Andreasen, Carsten Suhr Jacobsen
• Format: Article in Journal/Newspaper
• Language: English
• Published: Zenodo 2019
• Subjects: Arctic
• Online Access: https://doi.org/10.1093/gigascience/giz096

Metatranscriptomics has been used widely for investigation and quantification of microbial communities’ activity in response to external stimuli. By assessing the genes expressed, metatranscriptomics provides an understanding of the interactions between different major functional guilds and the environment. Here, we present ade novoassembly-based Comparative Metatranscriptomics Workflow (CoMW) implemented in a modular, reproducible structure. Metatranscriptomics typically uses short sequence reads, which can either be directly aligned to external reference databases (“assembly-free approach”) or first assembled into contigs before alignment (“assembly-based approach”). We also compare CoMW (assembly-based implementation) with an assembly-free alternative workflow, using simulated and real-world metatranscriptomes from Arctic and temperate terrestrial environments. We evaluate their accuracy in precision and recall using generic and specialized hierarchical protein databases.