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Run on GalaxyThis workflow constructs Metagenome-Assembled Genomes (MAGs) using SPAdes or MEGAHIT as assemblers, followed by binning with four different tools and refinement using Binette. The resulting MAGs are dereplicated across the entire input sample set, then annotated and evaluated for quality. You can provide pooled reads (for co-assembly/binning), individual read sets, or a combination of both. The input samples must consist of the original reads, which are used for abundance estimation. In all cases, reads should be trimmed, adapters removed, and cleaned of host or other contaminants before processing.
Steps
| ID | Name | Description |
|---|---|---|
| 17 | Unzip collection | __UNZIP_COLLECTION__ |
| 18 | Map parameter value | toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0 |
| 19 | Map parameter value | toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0 |
| 20 | MEGAHIT | toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2 |
| 21 | Run metaSPAdes in individual assembly mode | metaSPAdes performs co-assembly on default if multiple samples are supplied. This sub-WF allows running it individually. |
| 22 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 23 | Quast | toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1 |
| 24 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0 |
| 25 | CONCOCT: Cut up contigs | toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2 |
| 26 | Samtools sort | toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.7 |
| 27 | SemiBin | toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.1.0+galaxy1 |
| 28 | Calculate contig depths | toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0 |
| 29 | CONCOCT: Generate the input coverage table | toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2 |
| 30 | Converts genome bins in fasta format | toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1 |
| 31 | MaxBin2 | toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6 |
| 32 | MetaBAT2 | toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0 |
| 33 | CONCOCT | toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2 |
| 34 | Converts genome bins in fasta format | toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1 |
| 35 | Converts genome bins in fasta format | toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1 |
| 36 | CONCOCT: Merge cut clusters | toolshed.g2.bx.psu.edu/repos/iuc/concoct_merge_cut_up_clustering/concoct_merge_cut_up_clustering/1.1.0+galaxy2 |
| 37 | CONCOCT: Extract a fasta file | toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2 |
| 38 | Converts genome bins in fasta format | toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1 |
| 39 | Build list | __BUILD_LIST__ |
| 40 | Binette | toolshed.g2.bx.psu.edu/repos/iuc/binette/binette/1.2.0+galaxy0 |
| 41 | Pool Bins from all samples | __FLATTEN__ |
| 42 | checkm2 | toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.1.0+galaxy0 |
| 43 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2 |
| 44 | dRep dereplicate | toolshed.g2.bx.psu.edu/repos/iuc/drep_dereplicate/drep_dereplicate/3.6.2+galaxy1 |
| 45 | GTDB-Tk Classify genomes | toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk_classify_wf/gtdbtk_classify_wf/2.5.2+galaxy1 |
| 46 | CoverM genome | toolshed.g2.bx.psu.edu/repos/iuc/coverm_genome/coverm_genome/0.7.0+galaxy0 |
| 47 | CheckM lineage_wf | toolshed.g2.bx.psu.edu/repos/iuc/checkm_lineage_wf/checkm_lineage_wf/1.2.4+galaxy2 |
| 48 | Bakta | toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy1 |
| 49 | Quast | toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1 |
| 50 | checkm2 | toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.1.0+galaxy0 |
| 51 | Column join | toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 |
| 52 | Format Bakta output | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2 |
| 53 | Column join | toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 |
| 54 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy4 |
| 55 | Merge Bakta Output | toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 |
Version History
v0.1 (earliest) Created 30th Apr 2025 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.17986c0c
Creators and SubmitterViews: 3514 Downloads: 8865 Runs: 4
Created: 30th Apr 2025 at 03:02
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https://orcid.org/0000-0001-9852-1987
Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, nf-core
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