README.md

North Pacific Eukaryotic Gene Catalog (NPEGC)

Overview

The North Pacific Eukaryotic Gene Catalog (NPEGC) is a compilation of metatranscriptome sequence data and annotations derived from 261 samples collected from four oceanographic research cruises in the North Pacific Ocean.

Key Features

• 261 metatranscriptomes from five cruise studies
• 182 million transcript contigs (clustered at 99% protein identity)
• Taxonomic and functional annotations
• Read abundance data

Sample sites for metatranscriptomes in the North Pacific Eukaryotic Gene Catalog

Data Sources

1. Diel1: 48 samples from SCOPE HOE-Legacy 2 (July 2015) Diel 1 project page
2. Gradients1: 47 samples from KOK1606 (April-May 2016) Gradients 1 project page
3. Gradients2: 59 samples from MGL1704 (May-June 2017) Gradients 2 project page
4. Gradients3: 63 samples from KM1906 (April 2019) Gradients 3 project page
5. G3 diel: 44 samples from KM1906 (April 2019) G3 diel study project page

Data Products

1. Raw Metatranscriptome Assemblies

• Link to Zenodo repository

2. Processed Protein Contigs and Annotations

• Link to Zenodo repository

3. Processed Nucleotide Metatranscripts and Read Counts

• Link to Zenodo repository

Script Index

Universal Scripts

These scripts are used across all studies in the North Pacific Eukaryotic Gene Catalog:

1. Illumina_QC_AWS.sh: Description: Performs quality control and trimming of raw Illumina sequencing data using Trimmomatic.

2. NPEGC.6tr_frame_selection_clustering.sh: Translates nucleotide sequences, selects the longest coding frame(s), and clusters protein sequences at 99% identity.

3. NPEGC.diamond_taxonomy.log.sh: Assigns taxonomic identifiers to protein sequences using DIAMOND alignment against the MarFERReT + MARMICRODB database.

4. NPEGC.hmmer_function.sh: Annotates protein sequences with protein families using HMMER against the Pfam database.

5. NPEGC.nt_kallisto_counts.sh: Quantifies transcript abundances by aligning short reads to assembled transcripts using kallisto.

6. aggregate_kallisto_counts.R: Consolidates kallisto output files, joining sequence length and estimated count values for each project's metatranscriptome.

Study-Specific Scripts

Each study (G1PA, G2PA, G3PA, G3PA_diel, D1PA) has two specific scripts:

1. {STUDY_ID}.process_short_reads.sh: Performs quality control and preprocessing of raw sequencing data for the specific study.

2. {STUDY_ID}.trinity_assemblies.sh: Uses Trinity to perform de novo assembly of metatranscriptomes for the specific study.

Links to study-specific scripts:

• Gradients 1 (G1PA):

  • G1PA.process_short_reads.sh
  • G1PA.trinity_assemblies.sh

• Gradients 2 (G2PA):

  • G2PA.process_short_reads.sh
  • G2PA.trinity_assemblies.sh

• Gradients 3 (G3PA):

  • G3PA_UW.process_short_reads.sh
  • G3PA_UW.trinity_assemblies.sh

• G3 Diel (G3PA_diel):

  • G3PA_diel.process_short_reads.sh
  • G3PA_diel.trinity_assemblies.sh

• Diel1 (D1PA):

  • D1PA.process_short_reads.sh
  • D1PA.trinity_assemblies.sh

Associated Data

Additional metadata and associated datasets are available on the Simons CMAP ocean data portal.

• SCOPE Diel1 associated data: https://simonscmap.com/catalog/cruises/KM1513
• Gradients 1 associated data: https://simonscmap.com/catalog/cruises/KOK1606
• Gradients 2 associated data: https://simonscmap.com/catalog/cruises/MGL1704
• Gradients 3 associated data: https://simonscmap.com/catalog/cruises/KM1906

Additional metadata for the Gradients cruises can be found here: http://scope.soest.hawaii.edu/data/gradients/gradients.html

Citation

If you use this data in your research, please cite:

Groussman, R. D., Coesel, S. N., Durham, B. P., Schatz, M. J. & Armbrust, E. V. The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Sci. Data 11, 1161 (2024). doi:10.1038/s41597-024-04005-5