NGTax Version 7
Visit source
Download RO-CrateAmplicon analysis workflow using NG-Tax
Steps:
- Quality control on the reads
- Execute NGTax for ASV detection and classification
For more information about NG-Tax 2.0 have a look at https://doi.org/10.3389/fgene.2019.01366
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| files | file paths | files to download | string[] |
| destination | IRODS final destination | Final destination on iRODS | string |
| forward_primer | Forward primer | Forward primer used | string |
| reverse_primer | Reverse primer | Reverse primer used | string |
| reference_db | Reference database | Reference database used in FASTA format | string? |
| rev_read_len | Reverse read length | Read length of the reverse read | int |
| for_read_len | Reverse read length | Read length of the reverse read | int |
| sample | Sample name | Name of the sample being analysed | string |
Steps
| ID | Name | Description |
|---|---|---|
| irods_download | ||
| fastqc | ||
| ngtax |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| fastqc_output | n/a | n/a | Directory |
| ngtax_output | n/a | n/a | Directory |
Creators and Submitter
Views: 1905 Downloads: 54
Created: 23rd Jul 2020 at 10:59
Last updated: 8th Jun 2021 at 08:11
Last used: 16th Oct 2021 at 15:15
AttributionsNone
Version History
Version 7 (latest) Created 28th Oct 2020 at 11:07 by Jasper Koehorst
No revision comments
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, Genomics Coordination Center, 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
Web page: Not specified
An open infrastructure for exploring new horizons for research on microbial communities.
