Metagenomic Binning from Assembly
Visit source
Download RO-CrateWorkflow for Metagenomics binning from assembly
Minimal inputs are: Identifier, assembly (fasta) and a associated sorted BAM file
Summary
- MetaBAT2 (binning)
- MaxBin2 (binning)
- SemiBin (binning)
- DAS Tool (bin merging)
- EukRep (eukaryotic classification)
- CheckM (bin completeness and contamination)
- BUSCO (bin completeness)
- GTDB-Tk (bin taxonomic classification)
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default
All tool CWL files and other workflows can be found here:
Tools: https://gitlab.com/m-unlock/cwl
Workflows: https://gitlab.com/m-unlock/cwl/workflows
How to setup and use an UNLOCK workflow:
https://m-unlock.gitlab.io/docs/setup/setup.html
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 |
|
| assembly | Assembly fasta | Assembly in fasta format |
|
| bam_file | Bam file | Mapping file in sorted bam format containing reads mapped to the assembly |
|
| threads | Threads | Number of threads to use for computational processes |
|
| memory | memory usage (MB) | Maximum memory usage in megabytes |
|
| gtdbtk_data | gtdbtk data directory | Directory containing the GTDB database. When none is given GTDB-Tk will be skipped. |
|
| busco_data | BUSCO dataset | Directory containing the BUSCO dataset location. |
|
| run_semibin | Run SemiBin | Run with SemiBin binner |
|
| semibin_environment | SemiBin Environment | Semibin Built-in models (human_gut/dog_gut/ocean/soil/cat_gut/human_oral/mouse_gut/pig_gut/built_environment/wastewater/global/chicken_caecum) |
|
| sub_workflow | Sub workflow Run | Use this when you need the output bins as File[] for subsequent analysis workflow steps in another workflow. |
|
| step | CWL base step number | Step number for order of steps |
|
| destination | Output destination (not used in the workflow itself) | Optional output destination path for cwl-prov reporting. |
|
Steps
| ID | Name | Description |
|---|---|---|
| metabat2_contig_depths | contig depths | MetabatContigDepths to obtain the depth file used in the MetaBat2 and SemiBin binning process |
| eukrep | EukRep | EukRep, eukaryotic sequence classification |
| eukrep_stats | EukRep stats | EukRep fasta statistics |
| metabat2 | MetaBAT2 binning | Binning procedure using MetaBAT2 |
| metabat2_filter_bins | Keep MetaBAT2 genome bins | Only keep genome bin fasta files (exlude e.g TooShort.fa) |
| metabat2_contig2bin | MetaBAT2 to contig to bins | List the contigs and their corresponding bin. |
| maxbin2 | MaxBin2 binning | Binning procedure using MaxBin2 |
| maxbin2_to_folder | MaxBin2 bins to folder | Create folder with MaxBin2 bins |
| maxbin2_contig2bin | MaxBin2 to contig to bins | List the contigs and their corresponding bin. |
| semibin | Semibin binning | Binning procedure using SemiBin |
| semibin_contig2bin | SemiBin to contig to bins | List the contigs and their corresponding bin. |
| das_tool | DAS Tool integrate predictions from multiple binning tools | DAS Tool |
| das_tool_bins | Bin dir to files[] | DAS Tool bins folder to File array for further analysis |
| remove_unbinned | Remove unbinned | Remove unbinned fasta from bin directory. So analysed by subsequent tools. |
| checkm | CheckM | CheckM bin quality assessment |
| busco | BUSCO | BUSCO assembly completeness workflow |
| gtdbtk | GTDBTK | Taxomic assigment of bins with GTDB-Tk |
| compress_gtdbtk | Compress GTDB-Tk | Compress GTDB-Tk output folder |
| aggregate_bin_depths | Depths per bin | Depths per bin |
| bins_summary | Bins summary | Table of all bins and their statistics like size, contigs, completeness etc |
| bin_readstats | Bin and assembly read stats | Table general bin and assembly read mapping stats |
| metabat2_files_to_folder | MetaBAT2 output folder | Preparation of MetaBAT2 output files + unbinned contigs to a specific output folder |
| maxbin2_files_to_folder | MaxBin2 output folder | Preparation of maxbin2 output files to a specific output folder. |
| semibin_files_to_folder | SemiBin output folder | Preparation of SemiBin output files to a specific output folder. |
| das_tool_files_to_folder | DAS Tool output folder | Preparation of DAS Tool output files to a specific output folder. |
| checkm_files_to_folder | CheckM output | Preparation of CheckM output files to a specific output folder |
| busco_files_to_folder | BUSCO output folder | Preparation of BUSCO output files to a specific output folder |
| gtdbtk_files_to_folder | GTBD-Tk output folder | Preparation of GTDB-Tk output files to a specific output folder |
| output_bin_files | Bin files | Bin files for subsequent workflow runs when sub_worflow = true |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| bins | Bin files | Bins files in fasta format. To be be used in other workflows. |
|
| metabat2_output | MetaBAT2 | MetaBAT2 output directory |
|
| maxbin2_output | MaxBin2 | MaxBin2 output directory |
|
| semibin_output | SemiBin | MaxBin2 output directory |
|
| das_tool_output | DAS Tool | DAS Tool output directory |
|
| checkm_output | CheckM | CheckM output directory |
|
| busco_output | BUSCO | BUSCO output directory |
|
| gtdbtk_output | GTDB-Tk | GTDB-Tk output directory |
|
| bins_summary_table | Bins summary | Summary of info about the bins |
|
| bins_read_stats | Assembly/Bin read stats | General assembly and bin coverage |
|
| eukrep_fasta | EukRep fasta | EukRep eukaryotic classified contigs |
|
| eukrep_stats_file | EukRep stats | EukRep fasta statistics |
|
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: 13098 Downloads: 1961
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, 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, 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
Web page: Not specified
An open infrastructure for exploring new horizons for research on microbial communities.
