From Fastqs to VCFs and BAMs 1.0
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Associated Tutorial
This workflows is part of the tutorial Identifying tuberculosis transmission links: from SNPs to transmission clusters, available in the GTN
Thanks to...
Tutorial Author(s): Galo A. Goig, Daniela Brites, Christoph Stritt
Tutorial Contributor(s): Wolfgang Maier, Saskia Hiltemann, Helena Rasche, Galo A. Goig, Björn Grüning, Peter van Heusden, Christoph Stritt, Lucille Delisle
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Mycobacterium_tuberculosis_ancestral_reference.gbk | #main/Mycobacterium_tuberculosis_ancestral_reference.gbk | n/a |
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| Paired-End FASTQs | #main/Paired-End FASTQs | n/a |
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| Single-End FASTQs | #main/Single-End FASTQs | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Trimmomatic | toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 |
| 4 | Trimmomatic | toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 |
| 5 | Mapping and variant calling of SINGLE END FASTQs with snippy | toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 |
| 6 | Mapping and variant calling of PAIRED END FASTQs with snippy | toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0 |
| 7 | Merge PE/SE VCFs in a single collection with all samples | __MERGE_COLLECTION__ |
| 8 | Merge PE/SE BAMs in a single collection with all samples (Part the workflow "Identifying DR with TB-profiler) | __MERGE_COLLECTION__ |
| 9 | TB Variant Filter | toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
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| _anonymous_output_10 | #main/_anonymous_output_10 | n/a |
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| _anonymous_output_11 | #main/_anonymous_output_11 | n/a |
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| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
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| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
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| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
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| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
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| _anonymous_output_6 | #main/_anonymous_output_6 | n/a |
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| _anonymous_output_7 | #main/_anonymous_output_7 | n/a |
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| _anonymous_output_8 | #main/_anonymous_output_8 | n/a |
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| _anonymous_output_9 | #main/_anonymous_output_9 | n/a |
|
Version History
master
Creators and Submitter
Views: 1156 Downloads: 168 Runs: 0
Created: 2nd Jun 2025 at 10:59
AttributionsNone
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Organizations: Galaxy
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