Marine microbial eukaryote transcriptomes

Overview

This repository provides assemblies of a sub-set publicly available short read (Illumina 50bp PE) datasets of marine microbial eukaryotes. The raw data were generated by the Marine Microbial Eukaryote Transcriptome Sequencing Project (http://marinemicroeukaryotes.org/). This project provides its own set of assemblies (generated using the Abyss assembler). Since our work-flows are geared towards assemblies generated by the Trinity assembler, raw data were obtained from the following website http://marinemicroeukaryotes.org/ and assembled using Trinity (http://trinityrnaseq.sourceforge.net/)

For our purposes the raw data were directly assembled using Trinity (see README for version number) using the default settings. Several species/strains were assembled using all available Illumina libraries combined (see README). The identifiers of the raw data are provided and culture conditions of the organisms can be retrieved from http://marinemicroeukaryotes.org/ using the MMETSP ID (see README for list).

If you use these data please cite

Keeling, P.J. et al., 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing. PLoS Biology, 12:e1001889.

Grabherr, M.G. et al., 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29:644-652.

Funding

NSF Dimensions of Biodiversity Grant DEB-1046075