Data from: Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder
Data files
Jul 31, 2020 version files 2.82 GB
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001-V4-004A_S1_L001_R1_001.fastq.gz
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001-V4-004A_S1_L001_R2_001.fastq.gz
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002-V4-012A_S2_L001_R1_001.fastq.gz
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010-V4-143A_S10_L001_R1_001.fastq.gz
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010-V4-143A_S10_L001_R2_001.fastq.gz
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011-V4-151A_S11_L001_R1_001.fastq.gz
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011-V4-151A_S11_L001_R2_001.fastq.gz
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012-V4-159A_S12_L001_R1_001.fastq.gz
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012-V4-159A_S12_L001_R2_001.fastq.gz
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013-V4-167A_S13_L001_R1_001.fastq.gz
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015-V4-183A_S15_L001_R1_001.fastq.gz
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028-V4-166A_S28_L001_R1_001.fastq.gz
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028-V4-166A_S28_L001_R2_001.fastq.gz
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029-V4-167A_S29_L001_R1_001.fastq.gz
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032-V4-170A_S32_L001_R1_001.fastq.gz
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032-V4-170A_S32_L001_R2_001.fastq.gz
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039-CBR-5-01_S39_L001_R1_001.fastq.gz
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040-CBR-5-02_S40_L001_R1_001.fastq.gz
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040-CBR-5-02_S40_L001_R2_001.fastq.gz
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041-CBR-5-03_S41_L001_R1_001.fastq.gz
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041-CBR-5-03_S41_L001_R2_001.fastq.gz
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045-CBR-7-01_S45_L001_R1_001.fastq.gz
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045-CBR-7-01_S45_L001_R2_001.fastq.gz
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047-CBR-7-03_S47_L001_R1_001.fastq.gz
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047-CBR-7-03_S47_L001_R2_001.fastq.gz
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048-PCR-Nve_S48_L001_R1_001.fastq-2.gz
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048-PCR-Nve_S48_L001_R1_001.fastq.gz
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048-PCR-Nve_S48_L001_R2_001.fastq-2.gz
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048-PCR-Nve_S48_L001_R2_001.fastq.gz
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18S_zOTU_data.csv
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COI_V4_allzOTU_20190703.fasta
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COI_zOTU_data_incl_rarefied.csv
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Ext-Blank_S227_L001_R1_001.fastq.gz
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Ext-Blank_S227_L001_R2_001.fastq.gz
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Ext-Blank-2_S255_L001_R1_001.fastq.gz
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Ext-Blank-2_S255_L001_R2_001.fastq.gz
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Ext-Blank-mouse_S228_L001_R1_001.fastq.gz
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Ext-Blank-mouse_S228_L001_R2_001.fastq.gz
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Ext-Blank-mouse-2_S256_L001_R1_001.fastq.gz
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Ext-Blank-mouse-2_S256_L001_R2_001.fastq.gz
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Figures_and_Analyses_R_Markdown_2020-06-25.html
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firstroundsequencing_TagsCOI.csv
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morphology_data.csv
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PCR-Nve-1_S96_L001_R1_001.fastq.gz
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PCR-Nve-1_S96_L001_R2_001.fastq.gz
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PCR-Nve-2_S192_L001_R1_001.fastq.gz
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PCR-Nve-2_S192_L001_R2_001.fastq.gz
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PCR-Nve-3_S257_L001_R1_001.fastq.gz
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PCR-Nve-3_S257_L001_R2_001.fastq.gz
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Pipeline_processing.R
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sample_map_incl_rarefied.csv
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secondsequencing_TagsCOI.csv
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V4-004A_S4_L001_R1_001.fastq.gz
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V4-004A_S4_L001_R2_001.fastq.gz
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V4-005A_S5_L001_R1_001.fastq.gz
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V4-011A_S11_L001_R1_001.fastq.gz
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V4-012A_S12_L001_R1_001.fastq.gz
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V4-014A_S14_L001_R1_001.fastq.gz
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V4-015A_S15_L001_R1_001.fastq.gz
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V4-019A_S19_L001_R1_001.fastq.gz
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V4-025A_S25_L001_R1_001.fastq.gz
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V4-026A_S26_L001_R1_001.fastq.gz
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V4-027A_S27_L001_R1_001.fastq.gz
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V4-028A_S28_L001_R1_001.fastq.gz
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V4-028A_S28_L001_R2_001.fastq.gz
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V4-029A_S29_L001_R1_001.fastq.gz
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V4-03_S231_L001_R1_001.fastq.gz
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V4-166A_S100_L001_R1_001.fastq.gz
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V4-166A_S100_L001_R2_001.fastq.gz
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V4-167A_S101_L001_R1_001.fastq.gz
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V4-167A_S101_L001_R2_001.fastq.gz
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V4-168A_S102_L001_R1_001.fastq.gz
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V4-168A_S102_L001_R2_001.fastq.gz
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V4-169A_S103_L001_R1_001.fastq.gz
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V4-169A_S103_L001_R2_001.fastq.gz
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V4-17_S245_L001_R1_001.fastq.gz
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V4-17_S245_L001_R2_001.fastq.gz
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V4-170A_S104_L001_R1_001.fastq.gz
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V4-170A_S104_L001_R2_001.fastq.gz
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V4-171A_S105_L001_R1_001.fastq.gz
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V4-171A_S105_L001_R2_001.fastq.gz
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V4-172A_S106_L001_R1_001.fastq.gz
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V4-172A_S106_L001_R2_001.fastq.gz
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V4-173A_S107_L001_R1_001.fastq.gz
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V4-173A_S107_L001_R2_001.fastq.gz
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V4-174A_S108_L001_R1_001.fastq.gz
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V4-174A_S108_L001_R2_001.fastq.gz
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V4-175A_S109_L001_R1_001.fastq.gz
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V4-175A_S109_L001_R2_001.fastq.gz
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V4-176A_S110_L001_R1_001.fastq.gz
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V4-176A_S110_L001_R2_001.fastq.gz
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V4-177A_S111_L001_R1_001.fastq.gz
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V4-177A_S111_L001_R2_001.fastq.gz
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V4-178A_S112_L001_R1_001.fastq.gz
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V4-178A_S112_L001_R2_001.fastq.gz
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V4-179A_S113_L001_R1_001.fastq.gz
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V4-179A_S113_L001_R2_001.fastq.gz
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V4-18_S246_L001_R1_001.fastq.gz
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V4-18_S246_L001_R2_001.fastq.gz
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V4-180A_S114_L001_R1_001.fastq.gz
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V4-180A_S114_L001_R2_001.fastq.gz
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V4-181A_S115_L001_R1_001.fastq.gz
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V4-181A_S115_L001_R2_001.fastq.gz
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V4-182A_S116_L001_R1_001.fastq.gz
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V4-182A_S116_L001_R2_001.fastq.gz
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V4-183A_S117_L001_R1_001.fastq.gz
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V4-183A_S117_L001_R2_001.fastq.gz
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V4-184A_S118_L001_R1_001.fastq.gz
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V4-184A_S118_L001_R2_001.fastq.gz
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V4-185A_S119_L001_R1_001.fastq.gz
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V4-185A_S119_L001_R2_001.fastq.gz
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V4-186A_S120_L001_R1_001.fastq.gz
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V4-186A_S120_L001_R2_001.fastq.gz
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V4-19_S247_L001_R1_001.fastq.gz
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V4-19_S247_L001_R2_001.fastq.gz
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V4-20_S248_L001_R1_001.fastq.gz
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V4-20_S248_L001_R2_001.fastq.gz
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V4-21_S249_L001_R1_001.fastq.gz
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V4-21_S249_L001_R2_001.fastq.gz
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V4-22_S250_L001_R1_001.fastq.gz
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V4-22_S250_L001_R2_001.fastq.gz
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V4-23_S251_L001_R1_001.fastq.gz
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V4-23_S251_L001_R2_001.fastq.gz
Abstract
Methods
See materials and methods of Molecular Ecology paper "Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder"
Usage notes
All raw fastq files were uploaded (gz compressed). They originate from two separate sequencing runs - file names starting with "V4..." are from the first run, file names starting with e.g. "003_V4..." are from the second run. Sample specific tags are in the respective COITags.csv files.
The pipeline to process the raw data is in the file "Pipeline_processing.R".
The html output of the R markdown code to analyse the data (includes code for all figures and supplemental material) is in the file Figures_and_Analyses_R_Markdown_2020-06-25.html, and all processed data input files are provided in .csv or .fasta format.