Format of PR2 reference flat files

Last updated on 2023-04-06 documentation

List of files are provided for each release

Each version has a 3 number code: version_x.y.z, e.g. 5.1.0

Important note : All files are in UNIX format (end of lines are indicated Line Feed-LF only). Please see at the bottom of the file how to converts the files to Windows format (end of lines are CR+LF).

Files to assign metabarcodes

dada2

pr2_version_x.y.z_SSU_dada2.fasta.gz contains a dada2 format compatible training file

Mothur or Qiime

Two files:

pr2_version_x.y.z_SSU_mothur.fasta.gz contains all sequences in fasta format with the accession in the description line
pr2_version_x.y.z_SSU_mothur.tax.gz contains the taxonomy of each sequence separated from the accession number by a tabulation
Note :Qiime only use 7 taxonomical levels by default.

USEARCH or VSEARCH

pr2_version_x.y.z_SSU_UTAX.fasta.gz contains one fasta file with the accession number of the sequence and its full taxonomy on the description line in the UTAX format. It is suitable to use with USEARCH and VSEARCH.

DECIPHER training set

pr2_version_x.y.z_SSU.decipher.trained.rds is a DECIPHER training set using 3 iterations and a maximum of 20 sequences per species (LearnTaxa) that can be used with the DECIPHER IDTaxa function to assign metabarcodes. Use the readRDS() function of R to load the file.

Emu

Emu is a very efficient program to assign reads to a taxonomy database. It is in particular useful for long reads such as provided by Nanopore or PacBio sequencers.

pr2_version_x.y.z_emu.zip .The files provided starting on version 5.1.0 are those used to build the emu database which is done with the following command:

emu build-database pr2_version_5.1.0_emu.db --sequences pr2_version_5.1.0_emu.fasta --seq2tax pr2_version_5.1.0_emu_map.tsv --taxonomy-list pr2_version_5.1.0_emu_taxo.tsv

Other files

Taxonomy structure

pr2_version_x.y.z_taxonomy.xlsx

Fasta file

pr2_version_x.y.z_SSU_taxo_long.fasta.gz: contains accession number, the name of sequence and full taxonomy on the description line. It is suitable to build a local database for BLAST search

Full database as Excel file

pr2_version_x.y.z_merged.xlsx: Includes sequences, taxonomy and metadata.

Sequences annotated as chimeric

pr2_version_x.y.z_chimera.xlsx

Unassigned sequences

pr2_version_x.y.z_unassigned.xlsx
These SSU GenBank sequences are not part yet of the PR2 database. However some of them have been automatically assigned with AssignTaxa and version 4.14 of PR2 (see columns at the end of the xlsx file).
These sequences can be useful to add more sequences to a phylogenetic tree for example or annotate a specific taxonomic group.

Examples of format

mothur fasta

>AB353770.1.1740_U
ATGCTTGTCTCAAAGATTAAGCCATGCATGTCTCAGTATAAGCTTTTACATGGCGAAACTGCGAATGGCTCATTAAAACA
GTTACAGTTTATTTGAAGGTCATTTTCTACATGGATAACTGTGGTAATTCTAGAGCTAATACATGCGCCCAAACCCGACT
CCGTGGAAGGGTTGTATTTATTAGTTACAGAACCAACCCAGGTTCGCCTGGCCATTTGGTGATTCATAATAAACGAGCGA
ATTGCACAGCCTCAGCTGGCGATGTATCATTCAAGTTTCTGACCTATCAGCTTCCGACGGTAGGGTATTGGCCTACCGTG
GCAATGACGGGTAACGGAGAATTAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCTAAGGAAGGCAG
CAGGCGCGCAAATTACCCAATCCTGACACAGGGAGGTAGTGACAAGAAATAACAATACAGGGCAACCATGTCTTGTA`

mothur taxonomy

AB353770.1.1740_U
Eukaryota;Alveolata;Dinophyta;Dinophyceae;Dinophyceae_X;Dinophyceae_XX;Peridiniopsis;Peridiniopsis_kevei;
KC672520.1.1801_U
Eukaryota;Opisthokonta;Fungi;Ascomycota;Pezizomycotina;Leotiomycetes;Leotiomycetes_X;Leotiomycetes_X_sp.;

UTAX fasta

>AB353770.1.1740_U;tax=k:Eukaryota,d:Alveolata,p:Dinophyta,c:Dinophyceae,o:Dinophyceae_X,f:Dinophyceae_XX,g:Peridiniopsis,s:Peridiniopsis_kevei
ATGCTTGTCTCAAAGATTAAGCCATGCATGTCTCAGTATAAGCTTTTACATGGCGAAACTGCGAATGGCTCATTAAAACA
GTTACAGTTTATTTGAAGGTCATTTTCTACATGGATAACTGTGGTAATTCTAGAGCTAATACATGCGCCCAAACCCGACT
CCGTGGAAGGGTTGTATTTATTAGTTACAGAACCAACCCAGGTTCGCCTGGCCATTTGGTGATTCATAATAAACGAGCGA
ATTGCACAGCCTCAGCTGGCGATGTATCATTCAAGTTTCTGACCTATCAGCTTCCGACGGTAGGGTATTGGCCTACCGT

dada2 fasta

>Eukaryota;Alveolata;Dinophyta;Dinophyceae;Dinophyceae_X;Dinophyceae_XX;Peridiniopsis;Peridiniopsis_kevei;
ATGCTTGTCTCAAAGATTAAGCCATGCATGTCTCAGTATAAGCTTTTACATGGCGAAACTGCGAATGGCTCATTAAAACA
GTTACAGTTTATTTGAAGGTCATTTTCTACATGGATAACTGTGGTAATTCTAGAGCTAATACATGCGCCCAAACCCGACT

fasta long

>AB353770.1.1740_U||Eukaryota|Alveolata|Dinophyta|Dinophyceae|Dinophyceae_X|Dinophyceae_XX|Peridiniopsis|Peridiniopsis_kevei
ATGCTTGTCTCAAAGATTAAGCCATGCATGTCTCAGTATAAGCTTTTACATGGCGAAACTGCGAATGGCTCATTAAAACA
GTTACAGTTTATTTGAAGGTCATTTTCTACATGGATAACTGTGGTAATTCTAGAGCTAATACATGCGCCCAAACCCGACT
CCGTGGAAGGGTTGTATTTATTAGTTACAGAACCAACCCAGGTTCGCCTGGCCATTTGGTGATTCATAATAAACGAGCGA

merged

pr2_main_id	pr2_accession	genbank_accession	start	end	label	taxo_id.x	species	chimera	chimera_remark	added_date	added_version	removed_date	removed_version	edited_date	edited_version	edited_by	edited_remark	remark	taxo_id.y	kingdom	supergroup	division	class	order	family	genus	taxo_edited_date	taxo_edited_version	taxo_removed_date	taxo_removed_version	taxo_remark	reference	seq_id	sequence	sequence_length	ambiguities	pr2_metadata_id	gb_date	gb_locus	gb_definition	gb_organism	gb_strain	gb_culture_collection	gb_clone	gb_isolate	gb_isolation_source	gb_specimen_voucher	gb_host	gb_collection_date	gb_environmental_sample	gb_country	gb_lat_lon	gb_collected_by	gb_note	pubmed_id	gb_publication	gb_authors	gb_journal	eukref_name	eukref_env_material	eukref_env_biome	eukref_biotic_relationship	eukref_specific_host	eukref_geo_loc_name	pr2_sample_type	p2_sample_method	pr2_ocean	pr2_latitude	pr2_longitude	pr2_sequence_origin	pr2_size_fraction	pr2_size_fraction_min	pr2_size_fraction_max	metadata_remark	metadata_select	sequence_label
AB353770.1.1740_U	AB353770	1	1740	U	2014	Peridiniopsis_kevei												2014	Eukaryota	Alveolata	Dinophyta	Dinophyceae	Dinophyceae_X	Dinophyceae_XX	Peridiniopsis								ATGCTTGTCTCAAAGATTAAGCCATGCATGTCTCAGTATAAGCTTTTACATGGCGAAACTGCGAATGGCTCATTAAAACAGTTACAGTTTATTTGAAGGTCATTTTCTACATGGATAACTGTGGTAATTCTAGAGCTAATACATGCGCCCAAACCCGACTCCGTGGAAGGGTTGTATTTATTAGTTACAGAACCAACCCAGGTTCGCCTGGCCATTTGGTGATTCATAATAAACGAGCGAATTGCACAGCCTCAGCTGGCGATGTATCATTCAAGTTTCTGACCTATCAGCTTCCGACGGTAGGGTATTGGCCTACCGTGGCAATGACGGGTAACGGAGAATTAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCTAAGGAAGGCAGCAGGCGCGCAAATTACCCAATCCTGACACAGGGAGGTAGTGACAAGAAATAACAATACAGGGCAACCATGTCTTGTAATTGGAATGAGTAGAATTTAAATCCCTTTACGAGTATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGGATTTCTGTCGAAGGAGACCGGTCCGCCCTCTGGGTGAGTATCTGGATCTCTTTGGACATCTTCTTGGGGAACGTATCTGCACTTCATTGTGCGGTGCGGTACTCAAGACTTTTACTTTGAGGAAATTAGAGTGTTTCAAGCAGGCACACGCCTTGAATACATTAGCATGGAATAATAAGATAGGACCTCGGTTCTATTTTGTTGGTTTCTAGAGCTGAGGTAATGATTAATAGGGATAGTTGGGGGCATTCGTATTTAACTGTCAGAGGTGAAATTCTTGGATTTGTTAAAGACGGACTACTGCGAAAGCATTTGCCAAGGATGTTTTCATTGATCAAGAACGAAAGTTAGGGGATCGAAGACGATCAGATACCGTCGTAGTCTTAACCATAAACCATGCCGACTAGAGATTGGAGGTCGTTATCCGTACGACTCCTTCAGCACCTTATGAGAAATCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGATTGATAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTTAACCTGCTAAATAGTGACACATTACCCCGGTAATGTGGGTTACTTCTTAGAGGGACTTTGCGTGTCTAACGCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCTGCACGCGCGCTACACTGATGCGCTCAACGAGTTTATGACCTTGCCCGGAAGGGTTGGGTAATCTTGTTAAAACGCATCGTGATGGGGATAGATTATTGCAATTATTAATCTTCAACGAGGAATTCCTAGTAAGCGCGAGTCATCAGCTCGTGCTGATTAAGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGATTGAGTGATCCGGTGAATAATTCGGACCGCAGCATTTGTCAGTTCCTGACTCATGCCGTGGAAAGTCTAGTGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACA	1740	0	3830		PLN	Peridiniopsis cf. kevei gene for 18S rRNA, partial sequence.									26-juil.-03		Japan: Toyama, Tomi-iwa Canal Park

Converting files from UNIX to Windows format

All files are in UNIX format (end of lines are indicated Line Feed-LF only). File can be converted to Windows format (end of lines are CR+LF):

Install Notepad++
Open the files to convert (e.g. for mothur the .fasta and .tax files)

Convert the end of lines

Now the file should like the image below (red arrow)
Save the file under the same name by clicking on the disk icon (blue arrow)

Documentation Database Files