Longread 16S classification workflow Version 1
Visit source
Download RO-CrateWorkflow for quality assessment and taxonomic classification of amplicon long read sequences.
In addition files are exported to their respective subfolders for easier data management in a later stage.
Inputs are expected to be basecalled fastq files
Steps:
- NanoPlot read quality control, before and after filtering
- fastplong read quality and length filtering
- Emu abundance; species-level taxonomic abundance for full-length 16S read
Click and drag the diagram to pan, double click or use the controls to zoom.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| identifier | identifier used | Identifier for this dataset used in this workflow |
|
| reads | Read file | Read file in FASTA or FASTQ format (can be gz) |
|
| reference_db | Reference database | Reference database used in FASTA format |
|
| readtype | Read type | Type of read nanopore or pacbio. default nanopore |
|
| fastq_rich | Fastq rich (ONT) | Input fastq is generated by albacore, MinKNOW or guppy with additional information concerning channel and time. Used to creating more informative quality plots (default false) |
|
| threads | Number of threads | Number of threads to use for computational processes |
|
| skip_read_filter | Skip quality filtering | Skip quality reporting and filtering. (Default false) |
|
| disable_quality_filtering | Disable_quality_filtering | "Quality filtering is enabled by default. If this option is specified, quality filtering is disabled. Quality plots will still be generated when skip_read_filter is false. (Default false)" |
|
| qualified_quality_phred | Qualified_quality_phred | the quality value that a base is qualified. Default 8 means phred quality >=Q9 is qualified. |
|
| mean_qual | Mean quality | if one read's mean_qual quality score < mean_qual, then this read is discarded. (Default 10) |
|
| minimum_length | Minimum length required | Reads shorter will be discarded. (Default 1200) |
|
| length_limit | Maximum length limit | Reads longer than length_limit will be discarded. (Default 1600) |
|
| trim_front | Trim_front | Trimming how many bases in front for read. (Default not set, 0) |
|
| trim_tail | trim_tail | Trimming how many bases in tail for read. (Default not set, 0) |
|
| cut_front | Cut front | Move a sliding window from front (5') to tail, drop the bases in the window if its mean quality < threshold, stop otherwise. Default false |
|
| cut_tail | Cut tail | Move a sliding window from tail (3') to front, drop the bases in the window if its mean quality < threshold, stop otherwise Default false. |
|
| cut_window_size | Cut window size | The window size option shared by cut_front, cut_tail or cut_sliding. Range: 1~1000. Default 4 |
|
| cut_mean_quality | Cut mean quality | The mean quality requirement option shared by cut_front, cut_tail or cut_sliding. Range: 1~36. Default 20 |
|
| start_adapter | start_adapter | The adapter sequence at read start (5'). (Default auto-detect) |
|
| end_adapter | End adapter | The adapter sequence at read end (3'). (Default auto-detect) |
|
| adapter_fasta | Adapter fasta | Specify a FASTA file to trim both read ends by all the sequences in this FASTA file. (Default None) |
|
| disable_adapter_trimming | Disable adapter trimming | Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled. Default true |
|
| output_filtered_reads | Output filtered reads | Output filtered reads when filtering is applied. (Default false) |
|
| destination | Output Destination | Optional Output destination used for cwl-prov reporting. |
|
Steps
| ID | Name | Description |
|---|---|---|
| workflow_merge_reads | Merge paired reads | Creates a single file object. Also merges reads if multiple files are given. |
| workflow_longread_quality | Oxford Nanopore quality workflow | Quality, filtering and taxonomic classification workflow for Oxford Nanopore reads |
| emu | Emu abundance | Emu abundance; species-level taxonomic abundance for full-length 16S read |
| step_output_filtered_reads | Output reads | Step needed to output filtered reads. |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| quality_folder | NanoPlot | Folder with quality plots from Nanoplot |
|
| filtered_reads | n/a | Filtered reads output file |
|
| emu_abundance | Emu abundances | n/a |
|
| emu_read_assignment_distributions | Emu read assignment distribution | n/a |
|
| emu_unclassified | Emu unclassified | n/a |
|
Version History
Version 1 (earliest) Created 10th Sep 2025 at 13:31 by Bart Nijsse
Initial commit
Open
masterd20af19
Creators and Submitter
Views: 583 Downloads: 147
Created: 10th Sep 2025 at 13:30
Last updated: 10th Sep 2025 at 14:40
AttributionsNone
Related items
Teams: UNLOCK, Systems and Synthetic Biology
Organizations: UNLOCK, Wageningen University & Research
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, 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-Bioimage Analysis Support, 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, RenLabBioinformatics, Yongxin's team, PiFlow, HLee_SeoGroup, UFZ - Image Data Management and Processing Workflows, Korean Bioinformaticians, Into the deep, XChem, CPM, SocialGene, Research Data Management ICE-2, ObjectRecognition, LiDAR, FONDA II C2, Astroparticle Lab, FAIRagro M4.4, Kgerring, QuackenbushLab, Virus sequencing team, SOS, BioImage Informatics and Analysis Workflows, BoostNano, simblockflow, CSSB, Research on Workflow scheduling, Research Data1, CSUbioinformatics, CDPP, Mr., ASD-HRS, data management, FAIR_thesis: Marine acoustic data, CellBinDB, DEEP Lab, University of Amsterdam, SIMEXP, nf-pediatric Team, Kasmanas, Structural Variation Analysis, fuzzyworkflow, CausalCoxMGM Team, Tufts University Center for Cellular Agriculture (TUCCA), Test, CrustyBase, Applied Computational Cancer Research, Click-qPCR, BAID Team, FabianLab, Vector informatics and genomics group, AlmondBreedingLab, Artificial Design for Intelligent Breeding, ELIXIR Biodiversity Community, GROTIA, Biomedical_LLM, WhiteSymmetry, Hämatologie Labor Kiel, pakbaba, Metagenomics Analysis, MTB Bioinformatics Workflows, RTC Bioinformatics, CMG-GUTS, EI Papatheodorou Group, Metagenomics Analysis of Microbiome, ColoPola: A polarimetric imaging dataset for colorectal cancer detection, AI in Zhou Lab, CEPLAS, LTER-Italy, Gevaert Lab, Kendall-Theisen lab pipelines, High Performance Scientific Computing Laboratory (HPSC), Ensembl Metazoa and Plants, BiRD, Q-Dawn, AMRMALDI, Systems and Synthetic Biology, EI Core Bioinformatics Group, Values Shape Community, SolutionMake, GENEX, iPol, zxfenglab, Bioinformatics Unit IIS-FJD, omnibenchmark, BioX Fanatics, Li-Omics Lab, Metro Team, ZiemertLab, Song Lab, PanGIA, Holobionts Workflows, An Ideal Design for RNA-seq investigations into RPL, AMI2B Team, Institute for Hearing Technology and Acoustics (IHTA), Transcriptomics in unexplained recurrent pregnancy loss, E-MOBI / EKONOMIK MOBIL,S.R.L, Workflow Run Crate working group, datafun, BioFAIR
Web page: Not specified
An open infrastructure for exploring new horizons for research on microbial communities.
