Metagenomics Binning Workflow
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Download RO-CrateThis workflow is dependent on other CWL workflows, see the git repository for these.
Workflow for Metagenomics from raw reads to annotated bins.
Main Steps
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workflow_quality.cwl:
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FastQC (control)
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fastp (quality trimming)
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bbmap contamination filter
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SPAdes (Assembly)
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QUAST (Assembly quality report)
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BBmap (Read mapping to assembly)
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MetaBat2 (binning)
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CheckM (bin completeness and contamination)
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GTDB-Tk (bin taxonomic classification)
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| identifier | identifier used | Identifier for this dataset used in this workflow | string |
| forward_reads | forward reads | forward sequence file locally | File[] |
| reverse_reads | reverse reads | reverse sequence file locally | File[] |
| threads | number of threads | number of threads to use for computational processes | int? |
| memory | memory usage (mb) | maximum memory usage in megabytes | int? |
| pacbio_reads | pacbio reads | file with PacBio reads locally | File[]? |
| bbmap_reference | contamination reference file | bbmap reference fasta file for contamination filtering | string |
| run_gtdbtk | Run GTDB-Tk | Run GTDB-Tk taxonomic bin classification when true | boolean |
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 on assembled contigs |
| workflow_sam_to_sorted_bam | sam conversion to sorted bam | Sam file conversion to a sorted indexed bam file |
| workflow_contig_read_counts | samtools idxstats | Reports alignment summary statistics |
| workflow_metabat2_contig_depths | contig depths | MetabatContigDepths to obtain the depth file used in the MetaBat2 binning process |
| workflow_metabat2 | metabat2 binning | Binning procedure using metabat2 |
| workflow_aggregate_bins | Depths per bin | Depths per bin |
| workflow_bins_stats | Bin assembly stats | Table of all bins and there assembly statistics like N50 |
| workflow_getunbinned | unbinned_contigs | Get unbinned contigs fasta |
| workflow_bin_readstats | Bin and assembly read stats | Table general bin and assembly read mapping stats |
| workflow_checkm | CheckM | CheckM bin quality assessment |
| workflow_gtdbtk | GTDBTK | Taxomic assigment of bins with GTDB-Tk |
| workflow_compress_gtdbtk | Compress GTDB-Tk | Compress GTDB-Tk output folder |
| compress_spades | Spades compressed | Compress the large Spades assembly output files |
| spades_files_to_folder | SPADES output folder | Preparation of spades output files to a specific output folder |
| quast_files_to_folder | QUAST output folder | Preparation of quast output files to a specific output folder |
| sorted_bam_files_to_folder | Mapped reads output folder | Preparation of mapped reads (sorted bam files) to a specific output folder |
| metabat_files_to_folder | MetaBat2 output folder | 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 | GTBD-Tk output folder | Preparation of GTDB-Tk output files to a specific output folder |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| filtered_stats | Filtered statistics | Statistics on quality and preprocessing of the reads | Directory |
| spades_output | SPADES | Metagenome assembly output by SPADES | Directory |
| quast_output | QUAST | Quast analysis output folder | Directory |
| bam_output | BAM files | Mapping results in indexed BAM format | Directory |
| metabat2_output | MetaBat2 | MetaBat2 output directory | Directory |
| checkm_output | CheckM | CheckM output directory | Directory |
| gtdbtk_output | GTDB-Tk | GTDB-Tk output directory | Directory |
Creators and Submitter
Views: 1547 Downloads: 64
Created: 15th Oct 2020 at 14:55
Last updated: 19th Oct 2021 at 14:55
Last used: 27th Nov 2021 at 01:57
AttributionsNone
Version History
Version 11 (latest) Created 18th Oct 2021 at 10:49 by Jasper Koehorst
Added more binning and assembly reports
Version 10 Created 7th Jun 2021 at 18:34 by Jasper Koehorst
No revision comments
Version 9 Created 1st Jun 2021 at 11:43 by Jasper Koehorst
No revision comments
Version 8 Created 6th May 2021 at 07:03 by Jasper Koehorst
No revision comments
Version 7 Created 8th Jan 2021 at 10:15 by Jasper Koehorst
No revision comments
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https://orcid.org/0000-0001-8172-8981
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