FROGS News - June 2023


FROGS News - June 2023

FROGS v4.1.0 is available

FROGS v4.1.0 can be downloaded on :

For an easy installation there are :

This new version is available among others on

Platform Galaxy Command line
GenoToul Bioinfo yes yes
Migale yes yes
IFB yes yes

What has changed since the last version?

FROGS produces ASV:

“ASVs are identical denoised reads with as few as 1 base pair difference between variants, representing an inference of the biological sequences prior to amplification and sequencing errors (Callahan et al., 2017). ASVs are mainly formed through the two most popular denoising algorithms, DADA2 and UNOISE (Edgar, 2016). Although less frequently implemented in the pipeline, deblur (Amir et al. 2017) and obiclean (Boyer et al., 2016) are other denoising algorithms for ASVs formation. The OTU clustering approaches include a much wider set of algorithms across different software, which typically rely on global sequence similarities. Swarm (Mahe et al., 2022) is a notably different sequence clustering approach, which, while technically a clustering algorithm, may also be considered a denoising method when using the fastidious method with d=1. It relies on the maximum number of differences between reads (local linking threshold) and forms clusters that are resilient to input-order changes, thus creating stable, high-resolution features (herein referred to as swarm-clusters). When using the fastidious method with d=1, swarm aims to produce clusters centered around real biological sequences, where clusters represent sequence variants.”"

Since FROGS uses swarm (with the fastidious method with d=1) and strongly promotes denoising by chimera removal and cluster filtering, FROGS produces ASVs.

As a result, we have modified all the terminology and changed two tool names:

Modified tools:

More readability on the 7 basic steps

For more readability, now the 7 basic steps are named:

  1. FROGS_0 Demultiplex reads: attributes reads to samples in function of inner barcode
  2. FROGS_1 Pre-process: merging, denoising and dereplication
  3. FROGS_2 Clustering swarm: produces single-linkage clustering on sequences
  4. FROGS_3 Remove chimera: removes PCR chimera in each sample
  5. FROGS_4 Cluster filters: filters clusters on several criteria
  6. FROGS_5 Taxonomic affiliation: produces taxonomic affiliation of each ASV’s seed by RDPtools and BLAST
  7. FROGS_6_Affiliation_Stat: processes some metrics on taxonomies

:books: Tutorials are available for FROGS_3 Remove chimera and FROGS_4 Cluster filters tools :

FROGS_1 Pre-process:

FROGS_1 Pre-process filters and dereplicates amplicons for use in diversity analysis. Now, this tool takes in charge long reads, you can choose between:

Functional inference:

The 4 FROGSFUNC tools are now 3 FROGSFUNC tools

Also, we fixed some bugs and improve the tools and their outputs. We have added companion graphics to help with the decision making process.

:books: Tutorials are available for these 3 tools :

Differential analysis:

The package DESeq2 provides methods to test for differential expression by use of negative binomial generalized linear models

Now, :exclamation: these two tools are available to analyse ASV or Function (from FROGSFUNC tools).

:books: Tutorials are available for these 2 tools :

Affiliation filter:

This tool removes or keeps ASVs or hides taxonomical metadata according to one or more criteria:

Now, user can choose to filter based on affiliation keyword in keeping all ASVs with the keyword. Before, user could only ignore ASVs with the keyword.

Here, user will ignore all ASVs with “Firmicutes” in its taxonomic affiliation.

Here, user will keep all ASVs with “Firmicutes” in its taxonomic affiliation.

:books: Tutorials are available for this tool :

New documentations for using FROGS v4.1.0:

New databases are available, here are all the databases we have formatted (on demand) for RDPClassifier and NCBI Blast+
Please pay attention to the licence of the database and how to cite it.

amplicon base filters version galaxy_value
ITS UNITE Eukaryote 9.0 ITS_UNITE_Eukayote_9.0
ITS UNITE Fungi 9.0 ITS_UNITE_Fungi_9.0
23S microgreen-db algae 1.2 23S_microgreen-db_algae_v1.2
23S microgreen-db ncbi 1.2 23S_microgreen-db_ncbi_v1.2
23S microgreen-db pr2-silva 1.2 23S_microgreen-db_pr2-silva_v1.2
rbcL Diat.barcode 11.1 rbcL_Diat.barcode_11.1
18S Diat.barcode 11.1 18S_Diat.barcode_11.1
COI COInr 2022_05_06 COI_COInr_2022_05_06

You need help to use FROGS, you are looking for training:

Please contact

And/or visit:
for a webinar training:
:exclamation: next session: 9th to 12th October 2023

for a presential training at Jouy-en-Josas:
:exclamation: next session: 10th to 14th September 2023

Who uses FROGS?

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A work by FROGS team