Skip to content

Latest commit

 

History

History
executable file
·
124 lines (69 loc) · 5.21 KB

RELEASE_NOTE.md

File metadata and controls

executable file
·
124 lines (69 loc) · 5.21 KB
Raw

v4.1.0+galaxy1 [DEV]

This version refers to FROGS_4.1.0 suit.

Function added:

  • Preprocess : can deal with longreads sequencing

v4.0.1+galaxy1 [2022-06]

Bug corrected:

  • Clustering : change output format for swarm_composition file from .tsv to .txt

v4.0.0+galaxy1 [2022-05]

Tools added:

PICRUSt2 is a software for predicting functional abundances based only on marker gene sequences. These tools are integrated in FROGS suite as FROGSFunc tools. They are splitted into 4 steps :

  • frogsfunc_step1_placeseqs : places the OTUs into a reference phylogenetic tree.
  • frogsfunc_step2_copynumbers : predicts marker and function copy number of each OTU.
  • frogsfunc_step3_functions : calculates functions abundances in each sample.
  • frogsfunc_step4_pathways : calculates pathway abundances in each sample.

Function added

  • Normalisation :
    • add "Sampling by the number of sequences of the smallest sample" sampling method. This method automatically detects the sample with the smallest number of sequences, and samples all other samples with that number.
    • If you chose "Select a number of reads" sampling method, you may or not activate "Remove samples" option. If it's activated, samples whose total number of sequences is lower than the specified number, will be removed from the abundance table. If the option is disabled, the samples will be kept in the analysis but with a number of sequences lower than the specified number (the total number of the sample).
  • Otu_filter : add "Replicate identification" Minimum prevalence method. It allows to keep OTUs present in miniam replication proportions in at least one group (must be a proportion between 0 and 1).
  • Affiliation_stat : add OTU rarefaction curves in HTML, in addition to the previously existing taxonomic ranks.
  • Remove_chimera : add "% Clusters kept" and "% Cluster abundance kept" in HTML chimera detection by sample table.

Bug corrected:

  • Affiliation_OTU : do not perform Needlall alignment if reduced reference database constructing by blasting R1 and R2 part of FROGS_combined OTU sequences is empty

v3.2.3+galaxy2 [2021-06]

This version still refers to FROGS_3.2.3 suit.

Modifications:

with help of @lecorguille

  • clean up xml code by using single quote, or python code following pep8 recommandations

  • init macros for version, requirement, logo and help

  • setup github actions for automatic galaxy testing

  • precise XML test sections

  • FROGS datamanager have been uploaded independently on the toolshed : https://toolshed.g2.bx.psu.edu/view/frogs/data_manager_frogs See README to remove previous installation of the datamanager without loosing previous reference databases downloaded.

v3.2.3.1 [2021-06]

This version still refers to FROGS_3.2.3 suit.

Modifications:

  • DESeq2 visualisation : correctly use the reference modality (in the tool conf pannel) as the expected modality2 in the deseq2_visualisation.py command line. Results were correct in the previous version but the reference condition was not the one precised by the user.

v3.2.3 [2021-06]

Modifications:

  • Affiliation_OTU : add a taxonomic rank parameter to correctly take into account taxonomy not defined on commonly used 7 ranks.
  • Update R and package dependencies to version 4.0.5 (because of trouble installing DESeq2 version 1.26).
  • Rename OTU FIlter and Affiliation Filter output files.

v3.2.2 [2021-04]

Tools added:

  • DESeq2 preprocess : Compute differential abundancy analysis
  • DESeq2 visualisation : 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.
  • FROGS datamanager is now available to manage affiliation reference database (frogs_db.loc for affiliation_OTU tool) thanks to @davidchristiany.

Contaminant database added

  • add Arabidopsis thaliana chroloroplast sequence

Modifications:

  • ITSx : add organism model option scanning, change default behavior regarding the trimming of conserved regions

  • Use english typo for normalise and visualise

  • rename phix_db.loc in contaminant_db.loc

  • update tool dependencies version

v3.1 [2018-01-08]

This release corresponds to the FROGS 3.1.0 release.

  • Tools added:

    • 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

  • Modifications:

    • use tool data table instead of simple loc files for filters, affiliation_OTU and affiliation_postprocess
    • Tree do no longer support Pynast alignment thanks to a template file

v2.0.0 [2018-12-11]

First package.

This release corresponds to the FROGS 2.0.0 release