Nanopore Guppy Basecalling Assembly Workflow Version 1
Visit source
Download RO Crate- deprecated -
Workflow for sequencing with ONT Nanopore, from basecalling to assembly.
- Guppy (basecalling of raw reads)
- MinIONQC (quality check)
- FASTQ merging from multi into one file
- Kraken2 (taxonomic classification)
- Krona (classification visualization)
- Flye (de novo assembly)
- Medaka (assembly polishing)
- QUAST (assembly quality reports)
All tool CWL files and other workflows can be found here:
Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl
Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| identifier | identifier used | Identifier for this dataset used in this workflow |
|
| threads | number of threads | number of threads to use for computational processes |
|
| fast5_files | nanopore reads | folder with Nanopore raw reads |
|
| configuration_command | n/a | n/a |
|
| kraken_database | n/a | database location of kraken2 |
|
| basecall_model | basecalling model | basecalling model used with Guppy |
|
Steps
| ID | Name | Description |
|---|---|---|
| workflow_basecalling | Guppy-CPU basecalling | Basecalling with Guppy for CPU of raw reads to FASTQ reads with summary |
| workflow_nanopore_noguppy | Nanopore workflow | The rest of the nanopore workflow without basecalling |
| guppy_files_to_folder | Guppy output folder | Preparation of Guppy output files to a specific output folder |
| workflow_minionqc | MinIONQC quality check | Plots and statistics generated with MinIONQC from basecalling with Guppy |
| minionqc_files_to_folder | MinIONQC output folder | Preparation of MinIONQC output files to a specific output folder |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| guppy_output | Guppy for CPU | Basecalling of raw reads with Guppy |
|
| minionqc_output | MinION-Quality-Check | Quality check of basecalling with MinIONQC |
|
| merge_output | FASTQ files merged | Concatenation of FASTQ files from Guppy |
|
| kraken2_output | Kraken2 reports | Kraken2 taxonomic classification reports |
|
| krona_output | Krona taxonomy visualization | Visual presentation in HTML of Kraken2 results |
|
| flye_output | Flye de novo assembler for single-molecule reads | Flye output directory |
|
| medaka_output | Medaka polisher | Polishing of Flye assembly |
|
| quast_output | QUAlity assessment | QUAST analysis output |
|
Version History
Version 1 (earliest) Created 6th Jan 2022 at 07:36 by Jasper Koehorst
Added/updated 1 files
Open
master62ee0fe
Creators and Submitter
Views: 2311 Downloads: 35
Created: 6th Jan 2022 at 07:36
Last updated: 2nd Nov 2022 at 15:03
TagsThis item has not yet been tagged.
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, 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, 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, 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, EuroScienceGateway, 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
Web page: Not specified
An open infrastructure for exploring new horizons for research on microbial communities.
