DOI: 10.5281/zenodo.16745474
title: Data that accompanies the JEDI paper

description: Description

This repository contains the datasets analysed for the application examples from the JEDI paper (ASV tables sections), the modified version of nf-core/ampliseq including the consensus merge pairs approach and curated reference databases for SSU V3 to V5 and V4 to V9 extracted from PR2 and SILVA reference databases.

ASV tables

AE1-ROSCOFF_ALGAE



AE1-ROSCOFF_ALGAE-sample_meta.tsv: tab-separated table describing the samples from the multi-cellular holobiont application example.

AE1-ROSCOFF_ALGAE-ssu-v4v5-main.zip: archive containing the scripts and parameter files to build the SSU V4V5 application example ASV table using nf-core/ampliseq. This code repository is also here

AE1-ROSCOFF_ALGAE-ssu_v4v5_ampliseq_table.tsv.gz: ASV table with 69 tab separated fields. ASV are identified by the md5 (asv_id) of their sequence, and were taxonomically assigned (kingdom to genus) with dada2's assignTaxonomy() using SILVA 138.1. The total read number (total) and the total number of occurrences (spread) for each ASV are indicated alongside the per sample read numbers (L1I1_AOUT_BACT_S101 to MOCK_2_BACT_S272).


AE1-TREC_RHIZO



AE1-TREC_RHIZO-ssu_v4v5_ampliseq_table.tsv.gz: ASV table with 97 tab separated fields. ASV are identified by the md5 (ASV_ID) of their sequence. The other columns (11254839220230404SC2A10 to 11254839220230404SC2H9) indicate for each ASV the number of reads in the corresponding sample. 

AE1-TREC_RHIZO-ssu_v4v5_asv_tax_pr2.tsv.gz: tab-separated table containing the dada's taxonomic assignment results from nf-core/ampliseq (Domain to Species) using PR2 5.0.0.

AE1-TREC_RHIZO-ssu_v4v5_asv_tax_silva.tsv.gz: tab-separated table cointaining the dada's taxonomic assignment results from nf-core/ampliseq (Kingdom to Species) using SILVA 138.2.


AE2-SOMLIT_ASTAN



AE2-SOMLIT_ASTAN-18s-v4-v1.0.0.zip: archive containing the scripts and parameter files to build the 18S V4 application example ASV table using nf-core/ampliseq. This code repository is also here

AE2-SOMLIT_ASTAN-18s_v4_ampliseq_table.tsv.gz: ASV table with 390 tab separated fields. ASV are identified by the md5 (asv_id) of their sequence, and were taxonomically assigned (domain to species) by nf-core/ampliseq with dada2's assignTaxonomy()and addSpecies() using PR2 5.0.0. The total read number (total) and the total number of occurrences (spread) for each ASV are indicated alongside the per sample read numbers (RA090107_02 to RA160202_3).  Sample names follow this pattern: RA{year}{month}{day}_{size fraction; 02 for 0.2-3µm and 3 for > 3 µm}.

AE2-SOMLIT_ASTAN-ssu-v4v5-main.zip: archive containing the scripts and parameter files to build the SSU V4V5 application example ASV table using nf-core/ampliseq. This code repository is also here.

AE2-SOMLIT_ASTAN-ssu_v4v5_ampliseq_table.tsv.gz: ASV table with 177 tab separated fields. ASV are identified by the md5 (asv_id) of their sequence, and were taxonomically assigned (domain to species) by nf-core/ampliseq with dada2's assignTaxonomy() and addSpecies() using PR2 5.0.0. The total read number (total) and the total number of occurrences (spread) for each ASV are indicated alongside the per sample read numbers (RA090107_02 to RA121221_3).  Sample names follow this pattern: RA{year}{month}{day}_{size fraction; 02 for 0.2-3µm and 3 for > 3 µm}.

AE2-SOMLIT_ASTAN-ssu_v4v5_asv_tax_silva.tsv.gz: tab-separated table cointaining the dada's taxonomic assignment results from nf-core/ampliseq (kingdom to species) using SILVA 138.


AE3-TREC



AE3-TREC-18s-v9-main.zip: archive containing the scripts and parameter files to build the 18S V9 application example ASV table using nf-core/ampliseq. This code repository is also here.

AE3-TREC-18s_v9_ampliseq_table.tsv.gz: ASV table with 73 tab separated fields. ASV are identified by the md5 (asv_id) of their sequence, and were taxonomically assigned (domain to species) with dada2's assignTaxonomy() using PR2 5.0.0. The total read number (total) and the total number of occurrences (spread) for each ASV are indicated alongside the per sample read numbers (SAMEA112489502_METAB_18S_V9_HF22HDSXC_UDI229_BID27 to SAMEA112561548_METAB_18S_V9_HF22HDSXC_UDI253_BID02). The first part of each sample name corresponds to the Biosample ID, so sample metadata can directly be retrieved at https://www.ebi.ac.uk/biosamples/ using this ID.

AE3-TREC-18s_v9_meta.txt: tab-separated table describing the 18S V9 samples from TREC application example.

AE3-TREC-ssu-v4v5-main.zip: archive containing the scripts and parameter files to build the 18S V9 application example ASV table using nf-core/ampliseq. This code repository is also here.

AE3-TREC-ssu_v4v5_ampliseq_table.tsv.gz: ASV table with 73 tab separated fields. ASV are identified by the md5 (asv_id) of their sequence, and were taxonomically assigned (domain to species) with dada2's assignTaxonomy() using PR2 5.0.0. The total read number (total) and the total number of occurrences (spread) for each ASV are indicated alongside the per sample read numbers (SAMEA112489502_METAB_16S_V4V5_HW5CMDRX3_UDI029_BID05 to SAMEA112561548_METAB_16S_V4V5_HW5CMDRX3_UDI077_BID02). The first part of each sample name corresponds to the Biosample ID, so sample metadata can directly be retrieved at https://www.ebi.ac.uk/biosamples/ using this ID.

AE3-TREC-ssu_v4v5_asv_tax_silva.tsv.gz: tab-separated table cointaining the dada's taxonomic assignment assignTaxonomy() results (kingdom to genus) using SILVA 138.1.

AE3-TREC-ssu_v4v5_meta.txt: tab-separated table describing the SSU V4V5 samples from TREC application example.


nf-core/ampliseq with consensus approach

A modified version of nf-core/ampliseq version 2.8 has been used to generate the ASV table for the Application Examples (AE). This modified version consists in adding a new way of merging reads to allow to recover both overlapping and non overlapping reads in one step. This modified version is contained in the archive: ampliseq-consensus-merge-pairs-approach.tar.gz and can also be accessed here. The consensus merge paris approach is now available in nf-core/ampliseq since version 2.13.

Curated reference databases

We have created curated reference databases that span distinct hypervariable regions of the SSU rRNA gene, specifically:



V3 to V5 region - 'V3V5'

V4 to V9 region - 'V4V9'


The databases were constructed by aligning sequences from both the PR2 and SILVA databases against the backbone SILVA SSU REF138.2 alignment and extracting those sequences that span the respective regions.

There are two versions of each of the databases, one that contains all sequences spanning the respective regions (REF_SQ) and one that retains only those affiliated with a taxonomically defined species (i.e. valid binomial nomenclature and not metagenome, or uncultured or alphanumeric strings)

You will find files for the two different databases types. Specifically:



*-seqs.fa = Sequences that span the respective variable regions

*-taxonomy.txt = Information connecting the species ID to the original reference database accession along with Species and full taxonomic lineage classifications


Complete list of files:



V3V5-REF_SP-seqs.fa.gz

V3V5-REF_SP-taxonomy.txt.gz

V3V5-REF_SQ-seqs.fa.gz

V3V5-REF_SQ-taxonomy.txt.gz

V4V9-REF_SP-seqs.fa.gz

V4V9-REF_SP-taxonomy.txt.gz

V4V9-REF_SQ-seqs.fa.gz

V4V9-REF_SQ-taxonomy.txt.gz