Version 2

Workflow Type: Galaxy

SINGLE-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.


  • For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
  • SELECT the mot ADAPTED VADR MODEL for annotation (see vadr parameters).


ID Name Description Type
Ploidy file (Y for happloid) Ploidy file (Y for happloid) n/a
  • File


ID Name Description
0 FASTA Width toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1
1 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
3 VADR - Viral Annotation DefineR toolshed.g2.bx.psu.edu/repos/ftouzain/vadr/vadr/0.1.1
4 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/
5 bcftools mpileup toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/
6 VarDict on virus toolshed.g2.bx.psu.edu/repos/iuc/vardict_java/vardict_java/1.8.3+galaxy1
7 bcftools call toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.4.0
8 vvv2_display: Display SNP proportions and CDS of an assembly in png image toolshed.g2.bx.psu.edu/repos/ftouzain/vvv2_display/vvv2_display/0.1.10
9 vcfutils_vcf2fq: convert vcf file to fastq file toolshed.g2.bx.psu.edu/repos/ftouzain/vcfutils_vcf2fq/vcfutils_vcf2fq/1.16
10 seqtk_seq fq2fa fastq2fasta conversion toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_seq/1.3.3


ID Name Description Type
_anonymous_output_1 _anonymous_output_1 n/a
  • File
_anonymous_output_3 _anonymous_output_3 n/a
  • File
_anonymous_output_4 _anonymous_output_4 n/a
  • File
_anonymous_output_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
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_anonymous_output_9 _anonymous_output_9 n/a
  • File
_anonymous_output_10 _anonymous_output_10 n/a
  • File
_anonymous_output_11 _anonymous_output_11 n/a
  • File

Version History

Version 2 (earliest) Created 27th Jun 2023 at 15:41 by Fabrice Touzain

Update vadr wrapper, vadr version. Use vadr '--glsearch --split --cpu 4' to limit memory issue (especially for sarscov2 model)

Open master a3c888c
help Creators and Submitter
  • Fabrice Touzain

Views: 1970   Downloads: 124

Created: 27th Jun 2023 at 15:41

Last updated: 2nd Oct 2023 at 14:32

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Total size: 247 KB
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