Metagenomic Binning from Assembly
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Download RO CrateWorkflow for Metagenomics from raw reads to annotated bins. Steps:
- workflow_quality.cwl:
- FastQC (control)
- fastp (trimming)
- Kraken2 (Taxonomic Read Classification
- SPAdes (Assembly)
- QUAST (Assembly quality report)
- BBmap (Read mapping to assembly)
- sam_to_bam (sam to indexed bam)
- metabatContigDepths (jgi_summarize_bam_contig_depths)
- MetaBat2 (binning)
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 |
|
| filter_rrna | rRNA filtering | rRNA read filtering using ... |
|
| 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 |
|
| gzip | gzip compression | input data is gzip compressed |
|
| kraken_database | Kraken2 database | database location of kraken2 |
|
| pacbio_reads | pacbio reads | file with PacBio reads locally |
|
Steps
| ID | Name | Description |
|---|---|---|
| workflow_quality | Quality and filtering workflow | Quality assessment of illumina reads with rRNA filtering option |
| workflow_kraken | Kraken2 workflow | Read classification using the kraken2 database |
| 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_merge_bam_files | Merging bam files | Merge multiple bam files obtained from the sam to bam conversion module |
| workflow_metabat_contig_depths | depth file from metabat2 | Execution of metabat2 to obtain the depth file used in the binning process |
| workflow_metabat | binning process | Binning procedure using metabat2 |
| kraken_files_to_folder | Kraken output | Preparation of kraken output files to a specific output folder |
| 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 | metabat output | Preparation of metabatt 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 |
|
| kraken2_output | KRAKEN2 | Classification output folder by kraken |
|
| 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 |
|
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: 7434 Downloads: 459
Created: 15th Oct 2020 at 14:55
Last updated: 2nd Nov 2022 at 15:29
AttributionsNone
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