v2.0.0

Tools added :

• Tree : perform phylogenetic tree reconstruction based on Mafft or Pynast follow by Fasttree and phangorn
• FROGS Phyloseq Import Data : import data from 3 files: biomfile, samplefile, treefile into a phyloseq R object.
• FROGS Phyloseq Composition Visualization with bar plot and composition plot
• FROGS Phyloseq Alpha Diversity with richness plot
• FROGS Phyloseq Beta Diversity distance matrix
• FROGS Phyloseq Structure
• FROGS Phyloseq Clustering
• FROGS Phyloseq Manova

libexec program added:

• rooted_tree.R : Rscript to root FastTree tree. (used by Tree)

Bugs fixes:

• Preprocess : min overlap at least equal to 1
• biom2tsv : not working with stdBiom containing RDP affiliation, not working when emtpy metadata

Functions added:

• Preprocess: add Flash mismatch rate option

v1.4.0

Bugs fixes:

• Preprocess: error in final dereplication with hudge number of samples.
• Remove_chimera: error when using library Queue and hudge number of samples.
• Clusters_stat: error with empty samples in hierarchical clustering.
• Filters: error when only the filter on contamination is used.
• Filters: bug when using other filters than abundance (check parameter when None).

Functions added:

• Preprocess: new amplicon length graph.
• Clustering: reduce memory consumption and execution time for the step swarm2biom.
• Affiliations_stat: more details in alignment heatmap.

v1.3.0

Update notes:

This section contain actions to execute if you update a previous FROGS version to this version.

• The directory lib has been created and librairies have been renamed. In installation step 2 if you have added FROGS/bin in the PYTHONPATH you can remove this path and add FROGS/lib instead.

• The directory libexec has been created. In installation step 2 if you have added FROGS/bin in the PATH you can remove this path and add FROGS/libexec instead.

• The tools are moved in app directory. If you use FROGS in galaxy you must change the tool_conf.xml:

  ...
  <section id="FROGS_wrappers" name="FROGS">
      <tool file="FROGS/app/upload_tar.xml" />
      <tool file="FROGS/app/demultiplex.xml" />
      <tool file="FROGS/app/preprocess.xml" />
      <tool file="FROGS/app/clustering.xml" />
      <tool file="FROGS/app/remove_chimera.xml" />  
      <tool file="FROGS/app/filters.xml" />
      <tool file="FROGS/app/affiliation_OTU.xml" />
      <tool file="FROGS/app/clusters_stat.xml" />
      <tool file="FROGS/app/affiliations_stat.xml" />
      <tool file="FROGS/app/biom_to_stdBiom.xml" />
      <tool file="FROGS/app/biom_to_tsv/biom_to_tsv.xml" />
      <tool file="FROGS/app/tsv_to_biom.xml" />
      <tool file="FROGS/app/normalisation.xml" />
  </section>
  ...
  

Bugs fixes:

• Preprocess: missing values in lengths distribution graph.

v1.2.0

Update notes:

This section contain actions to execute if you update a previous FROGS version to this version.

• The repository structure has been changed: tools have been moved in sub-directories. It is necessary to re-do the following installation steps: '6. Add tools in galaxy' and '7. Set memory and parallelisation settings'.
• The tool FROGS_tsv_to_biom has been added. It is necessary to add the following line in galaxy tool_conf.xml: <tool file="FROGS/tools/tsv_to_biom/tsv_to_biom.xml" />.

Bugs fixes:

• Too large number of temp files in clustering tool.
• Fix bug with BIOM without observation metadata in filters.
• Fix bug with heatmap hover in affiliations_stat.

Functions added:

• Add tool to convert a TSV file in BIOM file.
• Default BIOM becomes mono-line.
• Reduce the BIOM file size (identation 4 -> 2 in pretty_print).
• Change the repository structure (one directory by tool).
• Use biomTools in normalisation.
• Number of sampled sequences becomes required in normalisation tool.
• Add better wrapping for sample name fields in preprocess.
• Add check on minimum amplicon size value in preprocess.
• Add vsearch version in remove chimera log.
• Add cutadapt version in preprocess log.

v1.1.0

Bugs fixes:

• Fix bug with empty blast_taxonomy in BIOM.
• Fix bug with checkall in chrome.
• Fix bug with CSV extraction in HTML outputs.
• Fix bug 'Exception in thread QueueFeederThread' in slow systems.

Functions added:

• Add '% kept' in preprocess.
• Add checks on samples names in preprocess.
• Add DenseData management in BIOM.
• Add the biom1 datatype in tools.