Metagenomic Binning from Assembly

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Workflow Type: Common Workflow Language
Work-in-progress

Workflow 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.

SEEK ID: https://workflowhub.eu/workflows/64?version=9

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 Filer rRNA Filter rRNA from reads if 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
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
  • Directory
filter_output Filtered reads Reads filtered output folder
  • 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

Version History

Version 12 (latest) Created 3rd Oct 2025 at 11:18 by Bart Nijsse

Added annoation workflow. Changed bin refinement DAS Tool with Binette. Fixes and version bumps


Open master a5a293e

Version 11 Created 18th Oct 2021 at 10:49 by Jasper Koehorst

Added more binning and assembly reports


Open master d4c912c

Version 10 Created 7th Jun 2021 at 18:34 by Jasper Koehorst

No revision comments

Frozen master c2519b1

Version 9 Created 1st Jun 2021 at 11:43 by Jasper Koehorst

No revision comments

Frozen master d6fcbfa

Version 8 Created 6th May 2021 at 07:03 by Jasper Koehorst

No revision comments

Frozen master 0660405

Version 7 Created 8th Jan 2021 at 10:15 by Jasper Koehorst

No revision comments

Frozen master f3919f2
help Creators and Submitter
Creators
Submitter
Discussion Channel
GitLab Issues
Tools
MetaBAT 2
SemiBin
MaxBin
Binette
BUSCO
CheckM2
License
Creative Commons Zero v1.0 Universal (CC0-1.0)
Activity

Views: 18690   Downloads: 3514

Created: 15th Oct 2020 at 14:55

Last updated: 3rd Oct 2025 at 11:33

Annotated Properties
Topic annotations
Operation annotations
Scientific disciplines
Immunology and Microbiology
help Attributions

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Total size: 13.5 KB
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