Quality assessment, amplicon classification and functional prediction
Visit source
Download RO-CrateWorkflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2.
In addition files are exported to their respective subfolders for easier data management in a later stage.
Steps:
- FastQC (read quality control)
- NGTax 2.0
- Picrust 2
- Export module for ngtax
Click and drag the diagram to pan, double click or use the controls to zoom.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| forward_reads | forward reads | forward sequence file locally |
|
| reverse_reads | reverse reads | reverse sequence file locally |
|
| forward_primer | Forward primer | Forward primer used |
|
| reverse_primer | Reverse primer | Reverse primer used |
|
| reference_db | Reference database | Reference database used in FASTA format |
|
| rev_read_len | Reverse read length | Read length of the reverse read |
|
| for_read_len | Reverse read length | Read length of the reverse read |
|
| sample | Sample name | Name of the sample being analysed |
|
| fragment | Subfragment name | Subfragment that is being analysed (e.g. V1-V3 or V5-region) |
|
| primersRemoved | Primers are removed | Wether the primers are removed or not from the input files |
|
| threads | number of threads | number of threads to use for computational processes |
|
| metadata | Metadata file | UNLOCK assay metadata file |
|
Steps
| ID | Name | Description |
|---|---|---|
| fastqc | n/a | n/a |
| reads_to_folder | n/a | n/a |
| ngtax | n/a | n/a |
| ngtax_to_tsv-fasta | n/a | n/a |
| picrust2 | n/a | n/a |
| folder_compression | n/a | n/a |
| fastqc_files_to_folder | n/a | n/a |
| ngtax_files_to_folder | n/a | n/a |
| picrust_files_to_folder | n/a | n/a |
| phyloseq_files_to_folder | n/a | n/a |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| turtle | n/a | Used for other workflows |
|
| files_to_folder_fastqc | n/a | n/a |
|
| files_to_folder_ngtax | n/a | n/a |
|
| files_to_folder_picrust2 | n/a | n/a |
|
| files_to_folder_phyloseq | n/a | n/a |
|
Version History
Version 2 (latest) Created 30th Sep 2021 at 12:15 by Jasper Koehorst
Open
master6d18328
Version 1 (earliest) Created 30th Aug 2021 at 08:18 by Jasper Koehorst
Added/updated 1 files
Frozen
master
8002b92
Creators and Submitter
Views: 3311 Downloads: 535
Created: 30th Aug 2021 at 08:18
Last updated: 11th Oct 2021 at 13:50
Tags AttributionsNone
Related items
https://orcid.org/0000-0001-8172-8981
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, MOLGENIS, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC, Probabilistic graphical models, GenX, Snakemake-Workflows, ODA, IPK BIT, CO2MICS Lab, FAME, CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus, Quadram Institute Bioscience - Bioinformatics, HecatombDevelopment, Institute of Human Genetics, Testing RO Crates, Test Team, Applied Computational Biology at IEG/HMGU, INFRAFRONTIER workflows, OME, TransBioNet, OpenEBench, Bioinformatics and Biostatistics (BIO2 ) Core, VIB Bioinformatics Core, CRC Cohort, ICAN, MustafaVoh, Single Cell Unit, CO-Graph, emo-bon, TestEMBL-EBIOntology, CINECA, Toxicology community, Pitagora-Network, Workflows Australia, Medizinisches Proteom-Center, Medical Bioinformatics, AGRF BIO, EU-Openscreen, X-omics, ELIXIR Belgium, URGI, Size Inc, GA-VirReport Team, The Boucher Lab, Air Quality Prediction, pyiron, CAPSID, Edinburgh Genomics, Defragmentation TS, NBIS, Phytoplankton Analysis, Seq4AMR, Workflow registry test, Read2Map, SKM3, ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression, de.NBI Cloud, Meta-NanoSim, ILVO Plant Health, EMERGEN-BIOINFO, KircherLab, Apis-wings, BCCM_ULC, Dessimoz Lab, TRON gGmbH, GEMS at MLZ, Computational Science at HZDR, Big data in biomedicine, TRE-FX, MISTIC, Guigó lab, Statistical genetics, Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation, OLCF-WES, Bioinformatics Unit @ CRG, Bioinformatics Innovation Lab, BSC-CES, ELIXIR Proteomics, Black Ochre Data Labs, Zavolan Lab, Metabolomics-Reproducibility, Team Cardio, NGFF Tools, Bioinformatics workflows for life science, Workflows for geographic science, Pacific-deep-sea-sponges-microbiome, CSFG, SNAKE, Katdetectr, INFRAFRONTIER GmbH, PerMedCoE, Euro-BioImaging, EOSC-Life WP3 OC Team, cross RI project, ANSES-Ploufragan, SANBI Pathogen Bioinformatics, Biodata Analysis Group, DeSci Labs, Erasmus MC - Viroscience Bioinformatics, ARA-dev, Mendel Centre for Plant Genomics and Proteomics, Metagenomic tools, WorkflowEng, Polygenic Score Catalog, bpm, scNTImpute, Systems Biotechnology laboratory, Cimorgh IT solutions, MLme: Machine Learning Made Easy, Hurwitz Lab, Dioscuri TDA, Scipion CNB, System Biotechnology laboratory, yPublish - Bioinfo tools, NIH CFDE Playbook Workflow Partnership, MMV-Lab, EMBL-CBA, EBP-Nor, Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data, Bioinformatics Laboratory for Genomics and Biodiversity (LBGB), multi-analysis dFC, CholGen, RNA group, Plant Genomes Pipelines in Galaxy, Pathogen Genomic Laboratory, Chemical Data Lab, JiangLab, Pangenome database project, HP2NET - Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment, Center for Open Bioimage Analysis, Generalized Open-Source Workflows for Atomistic Molecular Dynamics Simulations of Viral Helicases, Historical DNA genome skimming, QCDIS, Peter Menzel's Team, NHM Clark group, ESRF Workflow System (Ewoks), Kalbe Bioinformatics, Nextflow4Metabolomics, GBCS, CEMCOF, Jackson Laboratory NGS-Ops, Schwartz Lab, BRAIN - Biomedical Research on Adult Intracranial Neoplasms, Cancer Therapeutics and Drug Safety, Deepdefense, Mid-Ohio Regional Planning Commission, MGSSB, Institute for Human Genetics and Genomic Medicine Aachen, FengTaoSMU, EGA, Plant-Food-Research-Open, KrauthammerLab, Geo Workflows, grassland pDT, FunGIALab, CRIM - Computer Research Institute of Montréal, Medvedeva Lab, Metagenlab, FAIR-EASE, Protein-protein and protein-nucleic acid binding site prediction research, Culhane Lab, IDUN - Drug Delivery and Sensing, Edge Computing DAG Task Scheduling Research Group, Stratum corneum nanotexture feature detection using deep learning and spatial analysis: a non-invasive tool for skin barrier assessment, COPO, Taudière group, ErasmusMC Clinical Bioinformatics, interTwin, fluid flow modeling, EnrichDO, WorkflowResearch, Application Security - Test Crypt4GH solutions
Web page: Not specified
An open infrastructure for exploring new horizons for research on microbial communities.
