README

Files generated for EukRef worshop - 2023 - Barcelona

PR2 version: 5.0.1

Files are in directory exports. There is a sub-directory for each taxonomic group.

Please note that there are two types of sequences:

• Sequences that have been annotated in PR2 and that are part of the released database
• Sequences that are not part of PR2 and that have been annotated automatically using the naive Bayes assignment as implemented in dada2 R package. The database used for assignment is PR2 version 5.0.1.

There are 3 files:

pr2_export.fas.gz

Contains the sequence labelled with the PR2 accession number

>JX988758.1.1807_U
TTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTATAAGCACCTTATACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATCGTTTATTTGATGATCTCTTGCTACTTGGATACCCGTGGT...
...

pr2_export.txt

• Contains information about each sequence that can be uploaded to TreeView or TreeViewer.
• Fields are separated by tabulation.
• Species that have been assigned automatically by dada2 are labelled with 1 in the column pr2_annotated

pr2_accession   domain  supergroup  division    subdivision class   order   family  genus   species pr2_annotated   gb_strain
AF265331.1.1123_U   Eukaryota   TSAR    Stramenopiles   Bigyra  Sagenista   Labyrinthulomycetes Amphifilaceae   Amphifila   Amphifila_marina    1    
AY082983.1.1879_U   Eukaryota   TSAR    Stramenopiles   Bigyra  Sagenista   Labyrinthulomycetes Amphifilaceae   Amphifila   Amphifila_sp.   1    
EF023442.1.1807_U   Eukaryota   TSAR    Stramenopiles   Bigyra  Sagenista   Labyrinthulomycetes Amphifilaceae   Amphifilaceae_X Amphifilaceae_X_sp. 1    
EF023338.1.1806_U   Eukaryota   TSAR    Stramenopiles   Bigyra  Sagenista   Labyrinthulomycetes Amphifilaceae   Amphifilaceae_X Amphifilaceae_X_sp. 1    
EF023208.1.1805_U   Eukaryota   TSAR    Stramenopiles   Bigyra  Sagenista   Labyrinthulomycetes Amphifilaceae   Amphifilaceae_X Amphifilaceae_X_sp. 1    
EF023658.1.1802_U   Eukaryota   TSAR    Stramenopiles   Bigyra  Sagenista   Labyrinthulomycetes Amphifilaceae   Amphifilaceae_X Amphifilaceae_X_sp. 1    
EF023821.1.1802_U   Eukaryota   TSAR    Stramenopiles   Bigyra  Sagenista   Labyrinthulomycetes Amphifilaceae   Amphifilaceae_X Amphifilaceae_X_sp. 1    

...

pr2_export.xlsx

This file contains two sheets:

Sheet “taxonomy”

This is a summary of the taxonomy with the number of sequences assigned to each species

supergroup	division	subdivision	class	order	family	genus	species	n
Archaeplastida	Picozoa	Picozoa_X	Picomonadea	Picomonadida	Picomonadidae	Picomonas	Picomonas_judraskeda	74
Archaeplastida	Picozoa	Picozoa_X	Picozoa_XX	Picozoa_XXX	Picozoa_XXXX	Picozoa_XXXXX	Picozoa_XXXXX_sp.	391

Sheet “metadata”

Contains all the metadata of the PR2 database.

Please see a complete list of the fields here

In addition columns:

• pr2_annotated is 1 if the sequence is part of the PR2 database and 0 if it is not been annotated
• species_old should not be changed if you edit the species column

Instructions to edit xlsx files

• Instructions

PR2 curation pipeline for EukRef workshop

PR2_Curation.Rmd

Groups exported

PR2-exports-stats.md