binning-evaluation/main
v1.1 (latest)

v1.1 (latest)

v1.0 (earliest)

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Workflow Type: Galaxy

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This workflow performs multi-algorithm metagenomic binning evaluation using CONCOCT, MetaBAT2, SemiBin, and MaxBin2, optimizes results with DAS Tool and Binette, and evaluates all binning outputs against a gold standard using the CAMI AMBER framework to generate comprehensive HTML reports and performance metrics.

SEEK ID: https://workflowhub.eu/workflows/2100?version=2

Inputs

ID	Name	Description	Type
Assemblies	Assemblies	n/a	File[]
Binette contamination weight	Binette contamination weight	Set the contamination weight for Binette	int
Binette min completeness	Binette min completeness	Set the minimum completeness for Binette	int
Biobox File	Biobox File	n/a	File[]
CONCOCT Kmer length	CONCOCT Kmer length	Set the Kmer length for CONCOCT	int
CONCOCT Percentage of variance	CONCOCT Percentage of variance	Set the percentage of variance explained by the principal components for the combined data for CONCOCT	int
CONCOCT Read length	CONCOCT Read length	Set the read length for coverage for CONCOCT	int
CONCOCT Seed	CONCOCT Seed	Set the seed for clustering	int
CONCOCT Sequence length threshold	CONCOCT Sequence length threshold	Set the length threshold for sequences for CONCOCT	int
CONCOCT max numbers of Cluster	CONCOCT max numbers of Cluster	Set the maximum number of clusters for the Variational Gaussian Mixture Model (VGMM) algorithm for CONCOCT	int
CONCOCT number of iterations	CONCOCT number of iterations	Set the number iterations for CONCOCT	int
DAS Tool max iterations	DAS Tool max iterations	Set the maximum of iterations after reaching the score threshold	int
DAS Tool penalty for duplicate	DAS Tool penalty for duplicate	Set the penalty for duplicate single copy gene per bin for DAS Tool	float
DAS Tool penalty megabins	DAS Tool penalty megabins	Set the penalty for megabins for DAS Tool	float
DAS Tool score threshold	DAS Tool score threshold	Set the score threshold until selection algorithm will keep selecting bins for DAS Tool	float
ML Threshold for SemiBin	ML Threshold for SemiBin	When no threshold is set (so no number) SemiBin will calculate the threshold on its own	int?
MaxBin2 min contig length	MaxBin2 min contig length	Set the minimum contig length for MaxBin2	int
MaxBin2 number of iteration	MaxBin2 number of iteration	Set the maximum Expectation-Maximization algorithm iteration number for MaxBin2	int
MaxBin2 probability threshold	MaxBin2 probability threshold	Set the probability threshold for EM final classification for MaxBin2	float
MetaBAT2 TNF probability	MetaBAT2 TNF probability	Set the TNF probability cutoff for building TNF graph for MetaBAT2	int
MetaBAT2 max number for edges	MetaBAT2 max number for edges	Set the maximum number of edges per node for MetaBAT2	int
MetaBAT2 mean coverage	MetaBAT2 mean coverage	Set the mean coverage of a contig in each library for binning for MetaBAT2	float
MetaBAT2 min score	MetaBAT2 min score	Set the minimum score of an edge for binning for MetaBAT2	int
MetaBAT2 min size of contig	MetaBAT2 min size of contig	Set the minimum size of a contig for binning for MetaBAT2	int
MetaBAT2 min total effective	MetaBAT2 min total effective	Set the minimum of total effective mean coverage of a contig for binning for MetBAT2	float
MetaBAT2 percentage for binning	MetaBAT2 percentage for binning	Set the percentage of good contigs considered for binning decided by connection among contigs for MetaBAT2	int
Reads	Reads	In forward and reverse strands	File[]
Seed	Seed	Set seed for binners	int
SemiBin Batch size	SemiBin Batch size	Set the batch size for SemiBin	int
SemiBin number of epochs	SemiBin number of epochs	Set the number of epoch for SemiBin	int

Steps

ID	Name	Description
30	Extract element identifiers	toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
31	CONCOCT: Cut up contigs	toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2
32	CAMI AMBER add length column	toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_add/cami_amber_add/2.0.7+galaxy0
33	Bowtie2	toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.5+galaxy0
34	Text reformatting	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3
35	Samtools sort	toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.8
36	Relabel identifiers	__RELABEL_FROM_FILE__
37	CONCOCT: Generate the input coverage table	toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2
38	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
39	SemiBin	toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.1.0+galaxy1
40	Extract element identifiers	toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
41	CONCOCT	toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2
42	MetaBAT2	toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0
43	MaxBin2	toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6
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	CAMI AMBER convert to biobox	toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0
46	Split file	toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2
47	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
48	Converts genome bins in fasta format	toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1
49	CAMI AMBER convert to biobox	toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0
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	CAMI AMBER convert to biobox	toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0
52	Parse parameter value	param_value_from_file
53	CONCOCT: Extract a fasta file	toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2
54	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
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	CAMI AMBER convert to biobox	toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0
57	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3
58	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3
59	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3
60	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3
61	DAS Tool	toolshed.g2.bx.psu.edu/repos/iuc/das_tool/das_tool/1.1.7+galaxy1
62	Build list	__BUILD_LIST__
63	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3
64	Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3
65	Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3
66	Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3
67	Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3
68	CAMI AMBER convert to biobox	toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0
69	Binette	toolshed.g2.bx.psu.edu/repos/iuc/binette/binette/1.2.1+galaxy0
70	Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3
71	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3
72	CAMI AMBER convert to biobox	toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0
73	Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3
74	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3
75	Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3
76	CAMI AMBER	toolshed.g2.bx.psu.edu/repos/iuc/cami_amber/cami_amber/2.0.7+galaxy0

Outputs

ID	Name	Description	Type
AMBER Genome Metric	AMBER Genome Metric	n/a	File
AMBER HTML Report	AMBER HTML Report	n/a	File
AMBER Bin Metric	AMBER Bin Metric	n/a	File
AMBER Result Table	AMBER Result Table	n/a	File