Metagenomic Binning from Assembly
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Download RO-CrateWorkflow for Metagenomics from raw reads to bins.
Steps:
-
workflow_quality.cwl:
-
FastQC (control) -
fastp (quality trimming) -
bbmap contamination filter -
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)
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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 | Run GTDB-Tk | Run GTDB-Tk taxonomic bin classification when 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 | Spades compressed | 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 |
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| bam_output | BAM files | Mapping results in indexed BAM format |
|
| metabat2_output | MetaBat2 | MetaBat2 output directory |
|
| checkm_output | CheckM | CheckM output directory |
|
| gtdbtk_output | GTDB-Tk | GTDB-Tk 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: 9580 Downloads: 987
Created: 15th Oct 2020 at 14:55
Last updated: 2nd Nov 2022 at 15:29
AttributionsNone
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