Allele-based Pathogen Identification

Microbiome - Variant calling and Consensus Building

Associated Tutorial

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

Features

Thanks to...

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[]
reference_genome_of_tested_strain	reference_genome_of_tested_strain	Can be built in the tool later	File
samples_profile	samples_profile	based on the lab preparation of the samples during sequencing, there should be a sample profile better than the other, to be chosen as an optional input to Minimap2. e.g. PacBio/Oxford Nanpore For more details check: https://github.com/lh3/minimap2?tab=readme-ov-file#use-cases	string?

Steps

ID	Name	Description
3	Convert compressed file to uncompressed.	CONVERTER_gz_to_uncompressed
4	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0
5	Clair3	toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/0.1.12+galaxy0
6	Samtools depth	toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2
7	Samtools coverage	toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.15.1+galaxy2
8	bcftools norm	toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1
9	Advanced Cut	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1
10	Remove beginning	Remove beginning1
11	SnpSift Filter	toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
12	Table Compute	toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0
13	Cut	Cut1
14	SnpSift Extract Fields	toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
15	bcftools consensus	toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy1
16	Select first	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1
17	Remove beginning	Remove beginning1
18	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
19	Count	Count1
20	Advanced Cut	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1
21	Cut	Cut1
22	Paste	Paste1
23	Select first	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1
24	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
25	Column Regex Find And Replace	toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3

Outputs

ID	Name	Description	Type
decompressed_rg_file	decompressed_rg_file	n/a	File
map_with_minimap2	map_with_minimap2	n/a	File
clair3_pileup_vcf	clair3_pileup_vcf	n/a	File
clair3_full_alignment_vcf	clair3_full_alignment_vcf	n/a	File
clair3_merged_output	clair3_merged_output	n/a	File
normalized_vcf_output	normalized_vcf_output	n/a	File
quality_filtered_vcf_output	quality_filtered_vcf_output	n/a	File
extracted_fields_from_the_vcf_output	extracted_fields_from_the_vcf_output	n/a	File
bcftools_consensus	bcftools_consensus	n/a	File
mapping_coverage_percentage_per_sample	mapping_coverage_percentage_per_sample	n/a	File
mapping_mean_depth_per_sample	mapping_mean_depth_per_sample	n/a	File
number_of_variants_per_sample	number_of_variants_per_sample	n/a	File

Allele-based Pathogen Identification
1.0

Associated Tutorial

Features

Thanks to...

Inputs

Steps

Outputs

Version History

1.0 (earliest) Created 25th Jun 2024 at 10:55 by Helena Rasche

Creators

Submitter

Allele-based Pathogen Identification 1.0

Associated Tutorial

Features

Thanks to...

Inputs

Steps

Outputs

Version History

1.0 (earliest) Created 25th Jun 2024 at 10:55 by Helena Rasche

Creators

Submitter

Related items

Allele-based Pathogen Identification
1.0