The main website where RiboGrove is hosted may be unavailable outside Belarus due to technical troubles and the overall disaster.
Hence this mirror has been created, and RiboGrove files are available through Dropbox.

Home / Release notes

RiboGrove release notes

Release 24.230 (2025-05-08). Latest release.

No significant differences from the previous release.
Go to release 24.230.

Release 23.229 (2025-03-13).

Coverage estimation for primer pairs for different V-regions: more archaeal primers added.
Go to release 23.229.

Release 22.228 (2025-01-14).

Starting with RiboGrove 22.228,

We publish coverage values for PCR primers pairs commonly used to amplify V-regions of archaeal 16S rRNA genes. See the section “Coverage of primer pairs for different V-regions of bacterial 16S rRNA genes” on a RiboGrove release page.
Metadata does not contain tables gene_seqs_statistics.tsv and discarded_gene_seqs_statistics.tsv, because they contain much redundant data: taxonomy and genome categories. This data is in the separate tables: taxonomy.tsv and categories.tsv. In place of the removed files, metadata now contains files gene_seqs_base_counts.tsv and discarded_gene_seqs_base_counts.tsv. One can still make a gene_seqs_statistics.tsv table using the script merge_bases_categories_taxonomy.py from ribogrove-tools.

Go to release 22.228.

Release 21.227 (2024-11-15).

No significant differences from the previous release.
Go to release 21.227.

Release 20.226 (2024-09-18).

No significant differences from the previous release.
Go to release 20.226.

Release 19.225 (2024-08-21).

No significant differences from the previous release.
Go to release 19.225.

Release 18.224 (2024-08-20).

No significant differences from the previous release.
Go to release 18.224.

Release 17.223 (2024-03-21).

No significant differences from the previous release.
Go to release 17.223.

Release 16.222 (2024-03-20).

No significant differences from the previous release.
Go to release 16.222.

Release 15.221 (2024-03-20).

No significant differences from the previous release.
Go to release 15.221.

Release 14.220 (2024-03-19).

No significant differences from the previous release.
Go to release 14.220.

Release 13.219 (2023-07-19).

Starting with RiboGrove 13.219, metadata contains file primer_pair_genomic_coverage.tsv. In this file you can find coverage values for different V-region-targeting PCR primer pairs for each bacterial phylum, class, order, family, genus, and species.

Go to release 13.219.

Release 12.218 (2023-05-15).

Starting with the release 12.218 we use the “bscore” metric instead of “tscore” for pivotal gene detection (the ribotyper program calculates the mtrics).
Deletion length threshold was changed from 10 to 15 b.p. Now, deletions larger than 15 b.p. are considered long enough to discard a sequence.

Go to release 12.218.

Release 11.217 (2023-03-21).

Starting with release 11.217:

Header format has been changed again, and this is the last time it changes. Now, Assembly accession numbers are used instead of Assembly IDs with a G_ prefix (e.g. GCF_004799645.1: instead of G_2580821:).
Redundant data has been removed from metadata files. Now, for example, instead of a taxonomy string for each gene, the taxonomy.tsv file contains a taxonomy string for each genome, thus reducing the file size.
File QIIME2-compatible-taxonomy.txt has been removed from metadata archive. You can easily make it with the script make_qiime_taxonomy_file.py from ribogrove-tools v11.217 and later.
The process of sequence filtering has been modified:
- we removed the step which searches the gene sequences for 16S rRNA conserved regions according to Martinez-Porchas M et al.
- now, the pipeline uses the ribotyper program from the Ribovore suite to detect pivotal genes, instead of cmscan.

Go to release 11.217.

Release 10.216 (2023-01-18).

Starting with RiboGrove 10.216 we use Rfam 14.9 for sequence filtering. In Rfam 14.9, the model RF00177 (Bacterial small subunit ribosomal RNA) is updated. Before RiboGrove 10.216 we used Rfam 14.6.

Go to release 10.216.

Release 9.215 (2022-11-30).

Starting with release 9.215, we publish section “Coverage of primer pairs for different V-regions of bacterial 16S rRNA genes”.

Go to release 9.215.

Release 8.214 (2022-10-13).

Starting with release 8.214:

RiboGrove uses a new format of fasta headers to improve search specificity. Example:
Old header:
>NZ_CP009686.1:8908-10459_plus Bacillus_cereus ;Bacteria;Firmicutes;Bacilli;Bacillales;Bacillaceae;Bacillus; category:1
New header:
>G_324861:NZ_CP009686.1:8908-10459:plus ;d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus;s__cereus; category:1
Please, see the 8.214 release page for details.
We don’t publish fasta file of “raw” gene sequences any more because its content is mostly the same as data stored in the fasta file of full-length sequences.
To replace the “raw” fasta file, metadata now contains file discarded_sequences.fasta.gz. This file contains 16S rRNA gene sequences which were present in source RefSeq genomes and were annotated as 16S rRNA genes but which have been discarded according to their incompleteness, internal repeats etc. and thus haven’t been included in RiboGrove.
Metadata now does not contain files per_replicon_statistics.tsv and raw_per_replicon_statistics.tsv because of their unnecessary redundancy. All data they contained can be easily obtained from files gene_seqs_statistics.tsv and discarded_gene_seqs_statistics.tsv.

Go to release 8.214.

Release 7.213 (2022-07-20).

Starting with release 7.213, metadata contains the file QIIME2-compatible-taxonomy.txt. This is a TSV file, which can be used to train a QIIME2 classifier (see the tutorial).

Go to release 7.213.

Release 6.212 (2022-05-13).

No significant differences from the previous release.
Go to release 6.212.

Release 5.211 (2022-03-14).

No significant differences from the previous release.
Go to release 5.211.

Release 4.210 (2022-01-12).

No significant differences from the previous release.
Go to release 4.210.

Release 3.209 (2021-11-25).

The release date is correct: releases 2.208 and 3.209 were released on the same day.
Go to release 3.209.

Release 2.208 (2021-11-25)

The release date is correct: releases 2.208 and 3.209 were released on the same day.
Go to release 2.208.

Release 1.207 (2021-12-08)

You may wonder, why RiboGrove 1.207 was released on December 8^th, 2021, and RiboGrove 2.208 on November 25^th, 2021. The reason is that initially (on October 28^th, 2021), RiboGrove 1.207 wasn’t, strictly speaking, based on RefSeq 207 — it contained sequences, which had been added to RefSeq after release 207 but before release 208. The corrected version of RiboGrove 1.207 (2021-12-08) is based on RefSeq 207, without “contaminations” from RefSeq 208.

Go to release 1.207.

RiboGrove, 2024-09-18