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Repository frogs
Name: frogs
Owner: frogs
Synopsis: Suite for metabarcoding analysis
This is FROGS Galaxy Wrappers FROGS is a workflow designed to produce an ASV count matrix from high depth sequencing amplicon data. Adviced : reorder integrated_tool_panel.xml as indicated here : https://github.com/geraldinepascal/FROGS-wrappers#simplest-way 
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/frogs/frogs
Type: unrestricted
Revision: 8:0966b9635d76
This revision can be installed: True
Times cloned / installed: 654

Contents of this repository

Name Description Version Minimum Galaxy Version
perform Multivariate Analysis of Variance (MANOVA) 4.1.0+galaxy3 20.05
with heatmap plot and ordination plot 4.1.0+galaxy3 20.05
Attribute reads to samples in function of inner barcode 4.1.0+galaxy3 20.05
Normalise ASV abundance. 4.1.0+galaxy3 16.01
Remove PCR chimera in each sample 4.1.0+galaxy3 20.05
with bar plot and composition plot 4.1.0+galaxy3 20.05
Converts a TSV file in a BIOM file 1 4.1.0+galaxy3 20.05
from 3 files: biomfile, samplefile, treefile 4.1.0+galaxy3 20.05
Taxonomic affiliation of each ASV's seed by RDPtools and BLAST 4.1.0+galaxy3 20.05
Converts a BIOM file in TSV file 4.1.0+galaxy3 20.05
distance matrix 4.1.0+galaxy3 20.05
to extract and visualise differentially abundant ASVs or functions 4.1.0+galaxy3 20.05
Extract the highly variable ITS1 and ITS2 subregions from ITS sequences 4.1.0+galaxy3 20.05
Calculates functions abundances in each sample. 4.1.0+galaxy3 16.01
merging, denoising and dereplication 4.1.0+galaxy3 20.05
import a Phyloseq object and prepare it for DESeq2 differential abundance analysis 4.1.0+galaxy3 20.05
with richness plot 4.1.0+galaxy3 20.05
Places ASVs into a reference phylogenetic tree. 4.1.0+galaxy3 16.01
Process some metrics on clusters 4.1.0+galaxy3 20.05
Calculates pathway abundances in each sample. 4.1.0+galaxy3 16.01
Process some metrics on taxonomies 4.1.0+galaxy3 20.05
Filters clusters on several criteria. 4.1.0+galaxy3 16.01
Filters ASVs on several affiliation criteria 4.1.0+galaxy3 20.05
Single-linkage clustering on sequences 4.1.0+galaxy3 20.05
of samples using different linkage methods 4.1.0+galaxy3 20.05
Reconstruction of phylogenetic tree 4.1.0+galaxy3 20.05
Converts a FROGS BIOM in fully compatible BIOM 4.1.0+galaxy3 20.05
Aggregates ASVs based on alignment metrics 4.1.0+galaxy3 20.05

Categories
Metagenomics - Tools enabling the study of metagenomes