Gene-based Pathogen Identification

Nanopore datasets analysis - Phylogenetic Identification - antibiotic resistance genes detection and contigs building

Associated Tutorial

This workflows is part of the tutorial Gene-based Pathogen Identification, available in the GTN

Tutorial Author(s): Bérénice Batut, Engy Nasr, Paul Zierep

Tutorial Contributor(s): Hans-Rudolf Hotz, Wolfgang Maier

Workflow Author(s): Engy Nasr, Bérénice Batut, Paul Zierep

Funder(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health, EOSC-Life

Inputs

ID	Name	Description	Type
collection_of_preprocessed_samples	collection_of_preprocessed_samples	Output collection from the Nanopore Preprocessing workflow	File[]

Steps

ID	Name	Description
1	Extract element identifiers	toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
2	Build list	__BUILD_LIST__
3	Split file	toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0
4	Flye	toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0
5	Parse parameter value	param_value_from_file
6	medaka consensus pipeline	toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy0
7	Bandage Image	toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
8	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
9	FASTA-to-Tabular	toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
10	ABRicate	toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1
11	ABRicate	toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1
12	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
13	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
14	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
15	Tabular-to-FASTA	toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1

Outputs

ID	Name	Description	Type
extracted_samples_IDs	extracted_samples_IDs	n/a	File
list_of_lists_of_preprocessed_samples	list_of_lists_of_preprocessed_samples	n/a	File
splitted_extracted_samples_IDs	splitted_extracted_samples_IDs	n/a	File
flye_consensus_fasta	flye_consensus_fasta	n/a	File
flye_assembly_graph	flye_assembly_graph	n/a	File
flye_assembly_gfa	flye_assembly_gfa	n/a	File
flye_assembly_info_tabular	flye_assembly_info_tabular	n/a	File
parsed_extracted_samples_IDs_to_text	parsed_extracted_samples_IDs_to_text	n/a	File
medaka_gaps_in_draft_bed_file	medaka_gaps_in_draft_bed_file	n/a	File
medaka_log_file	medaka_log_file	n/a	File
medaka_propability_h5_file	medaka_propability_h5_file	n/a	File
medaka_calls_of_draft_bam_file	medaka_calls_of_draft_bam_file	n/a	File
sample_all_contigs	sample_all_contigs	n/a	File
bandage_assembly_graph_image	bandage_assembly_graph_image	n/a	File
sample_specific_contigs_tabular_file_preparation	sample_specific_contigs_tabular_file_preparation	n/a	File
abricate_with_vfdb_to_identify_genes_with_VFs	abricate_with_vfdb_to_identify_genes_with_VFs	n/a	File
abricate_report_using_ncbi_database_to_indentify_amr	abricate_report_using_ncbi_database_to_indentify_amr	n/a	File
sample_specific_contigs_tabular_file	sample_specific_contigs_tabular_file	n/a	File
vfs	vfs	n/a	File
amrs	amrs	n/a	File
contigs	contigs	n/a	File