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Picrust2 Functional Analysis

TASK
Typing name :  TASK.gws_ubiome.Picrust2FunctionalAnalysis Brick :  gws_ubiome v Parent : 

this task permit to predict functional analysis of 16s rRNA data

This task uses PICRUSt2 : Phylogenetic Investigation of Communities by Reconstruction of Unobserved States(paper can be found here).It wraps a number of tools to generate functional predictions based on 16S rRNA gene sequencing data. The input files should be a FASTA of amplicon sequences variants (ASVs; i.e. your representative sequences, not your raw reads, which is ASV-sequences.fasta generated using Q2FeatureInference task) and a qza table of the abundance of each ASV across each sample which is table.qza (generated using the same previous task ). The key output files are:

  • EC_metagenome_out : Folder containing unstratified EC number metagenome predictions. (pred_metagenome_unstrat.tsv.gz), sequence table normalized by predicted 16S copy number abundances. (seqtab_norm.tsv.gz), and the per-sample NSTI values weighted by the abundance of each ASV (weighted_nsti.tsv.gz).
  • KO_metagenome_out : As EC_metagenome_out above, but for Kegg orthology metagenomes.
  • pathways_out : Folder containing predicted pathway abundances and coverages per-sample, based on predicted EC number abundances.

Input

ASV_count_abundance
File containing the abundance of each ASV across each sample
FASTA_of_amplicon_sequences_variants
This file contain FASTA of amplicon sequences variants

Output

picrust2_out_pipeline
This folder contain the outputs

Configuration

num_processes

Optional

Number of threads

Type : intDefault value : 2