MarFERReT: an open-source, version-controlled reference library of marine microbial eukaryote functional genes
Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequence
Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of only about half of eukaryotic environmental transcripts. Here, we introduce version 1.0 of the Marine Functional EukaRyotic Reference Taxa (MarFERReT), an updated marine microbial eukaryotic sequence library with a version-controlled framework designed for taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 marine eukaryote genomes and transcriptomes from multiple sources and assessed these candidate entries for sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in the library. MarFERReT v1 contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. An accompanying MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.
MarFERReT is linked to a code repository hosting containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT here: https://github.com/armbrustlab/marferret
The raw source data for the 902 candidate entries considered for MarFERReT v1.1.1, including the 800 accepted entries, are available for download from their respective online locations. The source URL for each of the entries is listed here in MarFERReT.v1.1.1.entry_curation.csv, and detailed instructions and code for downloading the raw sequence data from source are available in the MarFERReT code repository (link).
This repository release contains MarFERReT database files from the v1.1.1 MarFERReT release using the following MarFERReT library build scripts: assemble_marferret.sh, pfam_annotate.sh, and build_diamond_db.sh
The following MarFERReT data products are available in this repository:
MarFERReT.v1.1.1.metadata.csv
This CSV file contains descriptors of each of the 902 database entries, including data source, taxonomy, and sequence descriptors. Data fields are as follows:
- entry_id: Unique MarFERReT sequence entry identifier.
- accepted: Acceptance into the final MarFERReT build (Y/N). The Y/N values can
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Files are hosted on the source repository. Click download to access the full dataset.