Allele-based Pathogen Identification 1.0
Visit source
Download RO-CrateMicrobiome - Variant calling and Consensus Building
Associated Tutorial
This workflows is part of the tutorial Allele-based Pathogen Identification, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
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 |
|
| reference_genome_of_tested_strain | reference_genome_of_tested_strain | Can be built in the tool later |
|
| 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 |
|
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 |
|
| map_with_minimap2 | map_with_minimap2 | n/a |
|
| clair3_pileup_vcf | clair3_pileup_vcf | n/a |
|
| clair3_full_alignment_vcf | clair3_full_alignment_vcf | n/a |
|
| clair3_merged_output | clair3_merged_output | n/a |
|
| normalized_vcf_output | normalized_vcf_output | n/a |
|
| quality_filtered_vcf_output | quality_filtered_vcf_output | n/a |
|
| extracted_fields_from_the_vcf_output | extracted_fields_from_the_vcf_output | n/a |
|
| bcftools_consensus | bcftools_consensus | n/a |
|
| mapping_coverage_percentage_per_sample | mapping_coverage_percentage_per_sample | n/a |
|
| mapping_mean_depth_per_sample | mapping_mean_depth_per_sample | n/a |
|
| number_of_variants_per_sample | number_of_variants_per_sample | n/a |
|
Version History
1.0 (earliest) Created 25th Jun 2024 at 10:55 by Helena Rasche
Added/updated 4 files
Open
mastera0c7ca8
Creators and Submitter
Views: 358 Downloads: 86
Created: 25th Jun 2024 at 10:55
Last updated: 25th Jun 2024 at 10:55
AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test
Web page: Not specified
Space: General
Public web page: https://galaxy.training
