mags-building/main
v0.5 (latest)

v0.5 (latest)

v0.4

v0.3

v0.2

v0.1 (earliest)

Workflow Type: Galaxy

This workflow performs metagenome assembly and multi-tool binning of paired short reads and optional long reads to generate dereplicated Metagenome-Assembled Genomes (MAGs), and analyzes them for quality and abundance.

SEEK ID: https://workflowhub.eu/workflows/1352?version=5

Inputs

ID	Name	Description	Type
ANI threshold for dereplication	ANI threshold for dereplication	ANI threshold to form secondary clusters of dereplication. An ANI value of ≥95-96% indicates genomes belong to the same species, an ANI of ≥98-99% suggests they are the same strain, and an ANI of ≤90-95% typically points to genomes from different genera.	float
CheckM2 Database	CheckM2 Database	CheckM2 Reference Database used for quality assessment for Binette, dRep, and quality assessment of the final bins	string
Choose Assembler	Choose Assembler	The workflow can use MEGAHIT and metaSPAdes as assembler	string
Contamination weight (Binette)	Contamination weight (Binette)	This weight is used for the scoring the bins. A low weight favor complete bins over low contaminated bins (--contamination_weight)	int
Custom Assemblies	Custom Assemblies	This workflow allows using a custom assembly as input. If provided, select `custom assembly` as Assembler. Provide one assembly for each group of trimmed input reads.	File[]?
Environment for the built-in model (SemiBin)	Environment for the built-in model (SemiBin)	Environment for the built-in model (SemiBin), options are: human_gut, dog_gut, ocean, soil, cat_gut, human_oral, mouse_gut, pig_gut, built_environment, wastewater, chicken_caecum, global	string
Maximum MAG contamination percentage	Maximum MAG contamination percentage	Maximum MAG contamination percentage for dereplication	int
Minimum MAG completeness percentage	Minimum MAG completeness percentage	Minimum MAG completeness percentage for bin refinement (binette) and dereplication (drep)	int
Minimum MAG length	Minimum MAG length	Minimum MAG length for dereplication	int
Minimum length of contigs to output	Minimum length of contigs to output	Minimum length of contigs to output (only for MEGAHIT).	int
Read length (CONCOCT)	Read length (CONCOCT)	CONCOCT requires the read length for coverage. Best use fastQC to estimate the mean value.	int
Run COMEBin	Run COMEBin	n/a	boolean
Trimmed PacBio reads from grouped samples	Trimmed PacBio reads from grouped samples	n/a	File[]?
Trimmed nanopore reads from grouped samples	Trimmed nanopore reads from grouped samples	n/a	File[]?
Trimmed paired reads from grouped samples	Trimmed paired reads from grouped samples	Samples grouped for co-assembly. For individual assembly use same reads as `Trimmed reads input`. The tool fastq_groupmerge can be used to perform the grouping.	File[]
Trimmed reads	Trimmed reads	These should be the reads from the samples to estimate MAGs abundance in the original samples.	File[]

Steps

ID	Name	Description
0	Create text file	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3
17	Select	Grep1
18	Extract element identifiers	toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
19	Apply rules	__APPLY_RULES__
20	Unzip collection	__UNZIP_COLLECTION__
21	Map parameter value	toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
22	Map parameter value	toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
23	Line/Word/Character count	wc_gnu
24	MEGAHIT	toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2
25	Parse parameter value	param_value_from_file
26	Duplicate file to collection	__DUPLICATE_FILE_TO_COLLECTION__
27	Relabel identifiers	__RELABEL_FROM_FILE__
28	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
29	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
30	Apply rules	__APPLY_RULES__
31	Apply rules	__APPLY_RULES__
32	Filter empty datasets	__FILTER_EMPTY_DATASETS__
33	Filter empty datasets	__FILTER_EMPTY_DATASETS__
34	metaSPAdes	toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.2.0+galaxy0
35	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
36	Quast	toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1
37	Bowtie2	toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0
38	CONCOCT: Cut up contigs	toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2
39	Samtools sort	toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.7
40	SemiBin latest	toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.1.0+galaxy1
41	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
42	Apply rules	__APPLY_RULES__
43	CONCOCT: Generate the input coverage table	toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2
44	Converts genome bins in fasta format	toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1
45	MaxBin2	toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6
46	MetaBAT2	toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0
47	COMEBin	toolshed.g2.bx.psu.edu/repos/iuc/comebin/comebin/1.0.4+galaxy1
48	CONCOCT	toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2
49	Converts genome bins in fasta format	toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1
50	Converts genome bins in fasta format	toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1
51	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
52	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
53	Converts genome bins in fasta format	toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1
54	CONCOCT: Extract a fasta file	toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2
55	Converts genome bins in fasta format	toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1
56	Build list	__BUILD_LIST__
57	Binette	toolshed.g2.bx.psu.edu/repos/iuc/binette/binette/1.2.0+galaxy0
58	Pool Bins from all samples	__FLATTEN__
59	checkm2	toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.1.0+galaxy0
60	Text reformatting	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2
61	dRep dereplicate	toolshed.g2.bx.psu.edu/repos/iuc/drep_dereplicate/drep_dereplicate/3.6.2+galaxy1
62	CoverM genome	toolshed.g2.bx.psu.edu/repos/iuc/coverm_genome/coverm_genome/0.7.0+galaxy0
63	CheckM lineage_wf	toolshed.g2.bx.psu.edu/repos/iuc/checkm_lineage_wf/checkm_lineage_wf/1.2.4+galaxy2
64	Quast	toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1
65	checkm2	toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.1.0+galaxy0
66	Column join	toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3
67	Column join	toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3
68	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy4

Outputs

ID	Name	Description	Type
metaSPAdes Contigs	metaSPAdes Contigs	n/a	File
Assembly Report	Assembly Report	n/a	File
Dereplicated Bins	Dereplicated Bins	n/a	File
Cluster Assignment	Cluster Assignment	n/a	File
Primary clustering dendrogram	Primary clustering dendrogram	n/a	File
Merged CoverM Output	Merged CoverM Output	n/a	File
Merged Quast Output	Merged Quast Output	n/a	File
Full MultiQC Report	Full MultiQC Report	n/a	File