- DESeq2 preprocess : Compute differential abundancy analysis
- DESeq2 visualization : Create table and plots to explore and illustrate the differential abundant OTUs
- Filters has been splitted into to new tools : FROGS OTU Filters and FROGS Affiliations Filters.
- FROGS OTU Filters filters OTU on presence/absence, abundances and contamination as Filters did. For contamination research, user may now use a personnal multifasta contaminant reference.
- FROGS Affiliation Filters delete OTU or mask affiliation that do not respect affiliation metrics criteria, or affiliated to undesirable (partial) taxon.
- Affiliation_postprocess : taxon-ignore option added, to ignore some taxon like "unknown species" during the aggreagation process. Multiple taxon may be provided as well as partial taxon, like "sp."
- Preprocess : now accept input sequence file as Fasta format (format automatically detected) for already contiged input.
- Affiliations_stat : check that the number of rank name correspond to the number of ranks in input biom file
- FROGSSTAT Phyloseq import : check sample names consistency between sample metadata and input biom file
- FROGS OTU Filters filters OTU on presence/absence, abundances and contamination as Filters did.
- Affiliation_postprocess : correctly compare de %coverage and the coverage threshold.
- FROGSSTAT Structure : plot_heatmap now take into account ordination method and dissimilarity matrix
- addAffiliation2biom : do not split partial description from blast reference ID
- tsv_2_biom now keep initial OTU order (Cluster_1 is the most abundant one and Cluster_X the less abundant one)
- FROGSSTAT Phyloseq and FROGSSTAT DESeq now generate notebook_html instead of classical HTML output file. This facilitates code maintenance.
- Tsv_to_Biom : manage quotes added by Excel
- Affiliation_postprocess : bug when references are not in the troncated amplicon database.
- Tree do no longer support Pynast alignment thanks to a template file
- XML wrappers, images and loc files are externalized to FROGS-wrappers (FROGS is now available on Toolshed and conda )
- ITSx : tool available for selecting and trimming ITS sequences based on ITSx tool
- Affiliation Postprocess : resolve ambiguities due to inclusiv ITS, and aggregated OTU based on taxonomic affiliations
- Preprocess : keep and filter non overlapped reads (particularly important for amplicon polymorphe in length)
- Affiliation : non overlapped read generate FROGS_combined OTU that are affiliated thanks to Needl (http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html) global alignment
- General : Use GALAXY_SLOTS variable in XML. Upadate version dependancies Remove redirection to /dev/null Update test/test.sh Update XML doc Update graphical charter of HTML outputs HTML reports now work on secured server by using of https instead of http to all JavaScript and CSS URLs (geraldinepascal#34).
- Preprocess : add VSEARCH and PEAR (https://sco.h-its.org/exelixis/web/software/pear/ only for command line usage because of PEAR licence) options to merge reads
- Clustering : deal with artificially combined reads
- FROGSSTAT tools do not call anymore external script from urls. Additionnal library dependancies added : https://github.com/mahendra-mariadassou/phyloseq-extended/releases
- FROGSSTAT import : can take FROGS specific biom file
- FROGS TSV_to_Biom : keeps original type of metadata (float, int or list instead of string) remove quotes added by Excel when exporting abundance tsv file in text file
- Phyloseq import: bug when Tree is None
- libexec/derepSamples : bug with temporary files name
- 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
- rooted_tree.R : Rscript to root FastTree tree. (used by Tree)
- Preprocess : min overlap at least equal to 1
- biom2tsv : not working with stdBiom containing RDP affiliation, not working when emtpy metadata
- Preprocess: add Flash mismatch rate option
# v1.4.0 [2017-02-04]
- 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).
- Tsv2Biom : bug fix when using a tsv file comming from a standard biom file
- Affiliations_stat : bug in rarefaction step computation when sample are empty
- 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 [2016-04-18]
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/binin the PYTHONPATH you can remove this path and addFROGS/libinstead. -
The directory libexec has been created. In installation step 2 if you have added
FROGS/binin the PATH you can remove this path and addFROGS/libexecinstead. -
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> ...
- Preprocess: missing values in lengths distribution graph.
# v1.2.0 [2016-04-06]
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" />.
- 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.
- 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.
- 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.
- Add '% kept' in preprocess.
- Add checks on samples names in preprocess.
- Add DenseData management in BIOM.
- Add the biom1 datatype in tools.
First package.