To assemble or not to resemble—A validated Comparative Metatranscriptomics Workflow (CoMW)
- 1. Department of Environmental Science, Aarhus University RISØ Campus, Frederiksborgvej 399, 4000 Roskilde, Denmark
- 2. AZTI, Herrera Kaia, Portualdea z/g, 20110 Pasaia, Basque Country, Spain
- 3. Toke Bang-Andreasen Department of Environmental Science, Aarhus University RISØ Campus, Frederiksborgvej 399, 4000 Roskilde, Denmark
Description
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 a de novo assembly-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.
Files
anwar_gigascience.pdf
Files
(1.8 MB)
Name | Size | Download all |
---|---|---|
md5:540db6469c135e2be75ec3f12b364367
|
1.8 MB | Preview Download |