Metagenomic Binning from Assembly
Visit source
Download RO-CrateWorkflow for Metagenomics from raw reads to annotated bins. Steps:
-
workflow_quality.cwl: -
FastQC (control) -
fastp (quality trimming) -
bbmap contamination filter -
SPAdes (Assembly) -
QUAST (Assembly quality report) -
BBmap (Read mapping to assembly) -
MetaBat2 (binning) -
CheckM (bin completeness and contamination) -
GTDB-Tk (bin taxonomic classification)
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 |
|
| forward_reads | forward reads | forward sequence file locally |
|
| reverse_reads | reverse reads | reverse sequence file locally |
|
| threads | number of threads | number of threads to use for computational processes |
|
| memory | memory usage (mb) | maximum memory usage in megabytes |
|
| pacbio_reads | pacbio reads | file with PacBio reads locally |
|
| bbmap_reference | contamination reference file | bbmap reference fasta file for contamination filtering |
|
| run_gtdbtk | Filer rRNA | Filter rRNA from reads if true |
|
Steps
| ID | Name | Description |
|---|---|---|
| workflow_quality | Quality and filtering workflow | Quality assessment of illumina reads with rRNA filtering option |
| workflow_spades | SPADES assembly | Genome assembly using spades with illumina/pacbio reads |
| workflow_quast | Quast workflow | Genome assembly quality assessment using Quast |
| workflow_bbmap | bbmap read mapping | illumina read mapping using BBmap |
| workflow_sam_to_sorted_bam | sam conversion to sorted bam | sam file conversion to a sorted indexed bam file |
| workflow_metabat2_contig_depths | depth file from metabat2 | Execution of metabat2 to obtain the depth file used in the binning process |
| workflow_metabat2 | binning process | Binning procedure using metabat2 |
| workflow_checkm | CheckM | CheckM bin quality assessment |
| workflow_getunbinned | unbinned_contigs | Get unbinned contigs fasta |
| workflow_gtdbtk | GTDBTK | Taxomic assigment of bins with GTDB-Tk |
| workflow_compress_gtdbtk | Compress GTDB-Tk | Compress GTDB-Tk output folder |
| compress_spades | Compress | Compress the large spades files |
| spades_files_to_folder | SPADES output | Preparation of spades output files to a specific output folder |
| quast_files_to_folder | QUAST output | Preparation of quast output files to a specific output folder |
| sorted_bam_files_to_folder | BAM output | Preparation of bam files output to a specific output folder |
| metabat_files_to_folder | MetaBat2 output | Preparation of MetaBat2 output files + unbinned contigs to a specific output folder |
| checkm_files_to_folder | CheckM output | Preparation of CheckM output files to a specific output folder |
| gtdbtk_files_to_folder | gtdbtk output | Preparation of GTDB-Tk output files to a specific output folder |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| fastqc_output | FASTQC | Quality reporting by FASTQC |
|
| filter_output | Filtered reads | Reads filtered output folder |
|
| spades_output | SPADES | Metagenome assembly output by SPADES |
|
| quast_output | QUAST | Quast analysis output folder |
|
| bam_output | BAM files | Mapping results in indexed BAM format |
|
| metabat2_output | MetaBat2 | MetaBat2 output directory |
|
| checkm_output | CheckM | CheckM output directory |
|
Version History
Version 11 (latest) Created 18th Oct 2021 at 10:49 by Jasper Koehorst
Added more binning and assembly reports
Open
masterd4c912c
Version 10 Created 7th Jun 2021 at 18:34 by Jasper Koehorst
Frozen
master
c2519b1
Version 9 Created 1st Jun 2021 at 11:43 by Jasper Koehorst
Frozen
master
d6fcbfa
Version 8 Created 6th May 2021 at 07:03 by Jasper Koehorst
Frozen
master
0660405
Version 7 Created 8th Jan 2021 at 10:15 by Jasper Koehorst
Frozen
master
f3919f2
Creators and Submitter
Views: 9578 Downloads: 987
Created: 15th Oct 2020 at 14:55
Last updated: 2nd Nov 2022 at 15:29
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, 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
Web page: Not specified
An open infrastructure for exploring new horizons for research on microbial communities.
