vvv2_align_SE_bwamem2
Version 1

Workflow Type: Galaxy
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 (can be opened in Excel/LibreOffice)

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
  • File
Majority_consensus #main/Majority_consensus n/a
  • File
image of all variants, genes, proteins and coverage depth #main/image of all variants, genes, proteins and coverage depth n/a
  • File
tsv file of information for significant variants #main/tsv file of information for significant variants n/a
  • File

Version History

Version 1 (earliest) Created 19th Jun 2025 at 11:09 by Fabrice Touzain

Initial commit


Open master 2352d20
help Creators and Submitter
Creator
  • Fabrice Touzain
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: 89   Downloads: 14   Runs: 0

Created: 19th Jun 2025 at 11:08

Last updated: 19th Jun 2025 at 11:20

help Attributions

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Total size: 307 KB
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