Workflow Type: Galaxy
Open
Stable
Using:
- vadr annotation (virus model must be selected in options)
- vardict variant caller
- coverage depth Provides summarizing files:
- png image of variant calling with annotations and coverage depths
- tsv file with all information of significant variants only
Steps
ID | Name | Description |
---|---|---|
0 | FASTA Width | toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2 |
1 | fastp | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 |
2 | VADR - Viral Annotation DefineR | toolshed.g2.bx.psu.edu/repos/ftouzain/vadr/vadr/0.2.0 |
3 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
4 | RmDup | toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 |
5 | bcftools mpileup | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy3 |
6 | VarDict | toolshed.g2.bx.psu.edu/repos/iuc/vardict_java/vardict_java/1.8.3+galaxy1 |
7 | Samtools depth | toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2 |
8 | bcftools call | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy3 |
9 | vvv2_display | - png image of variants - tsv file of variants info toolshed.g2.bx.psu.edu/repos/ftouzain/vvv2_display/vvv2_display/0.2.4.0 |
10 | IUPAC consensus | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3 |
11 | majority consensus | Gives consensus with major nucleotides only toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
IUPAC_consensus | #main/IUPAC_consensus | n/a |
|
Majority_consensus | #main/Majority_consensus | n/a |
|
image of all variants, genes, proteins and coverage depth | #main/image of all variants, genes, proteins and coverage depth | n/a |
|
tsv file of information for significant variants | #main/tsv file of information for significant variants | n/a |
|
Version History
Version 1 (earliest) Created 19th Jun 2025 at 11:14 by Fabrice Touzain
Initial commit
Open
master
078c3bf

Creator
Additional credit
This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne
Submitter
Activity
Views: 87 Downloads: 14 Runs: 1
Created: 19th Jun 2025 at 11:14
Last updated: 19th Jun 2025 at 11:23

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