Initially forked from here. Thank you to the awesome binder team!
Part of the Bioinformatics Virtual Coordination Network :)
This tutorial is a step-by-step guide on how to de novo assemble pared-end RNA reads.
Quality Control using FastQC and MultiQC
This tutorial will take you through the general advice provided for the Best practices for de novo transcriptome assembly with Trinity and show you how to assemble these quality trimmed and corrected reads with the de novo RNA assembler Trinity
We have provided two subsampled datasets from the following studies:
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Sieradzki, E., Ignacio-Espinoza, J.C., Needham, D. et al. Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes. Nat Commun 10, 1169 (2019). https://doi.org/10.1038/s41467-019-09106-z
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Husnik F, Nikoh N, Koga R, et al. Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis. Cell. 2013;153(7):1567-1578. https://doi:10.1016/j.cell.2013.05.040
Total dataset is available here https://www.ncbi.nlm.nih.gov/sra/SRX7867216[accn]
For more information see the following MicroSeminar talk
These two datasets represent vastly different ecosystems and are both provided to demonstrate the different challenges between de novo assembly of single organisms or more "simple" communities (2) verses de novo assembly of a metatranscriptome from more "complex" community assemblages (1).