Workflow Type: Galaxy

PAIRED-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 MOST 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
1 fastp
3 VADR - Viral Annotation DefineR
4 Map with BWA-MEM
5 bcftools mpileup
6 VarDict on virus
7 bcftools call
8 vvv2_display: Display SNP proportions and CDS of an assembly in png image
9 vcfutils_vcf2fq: convert vcf file to fastq file
10 seqtk_seq fq2fa fastq2fasta conversion


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
  • File
_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 28th Jun 2023 at 10:52 by Fabrice Touzain

Update vadr wrapper (use --glsearch --split --cpu 4) and vadr version (1.5.1) to limit memory usage (especially for sarscov2 model)

Open master 070a0c8
help Creators and Submitter
  • Fabrice Touzain

Views: 1075

Created: 28th Jun 2023 at 10:52

Last updated: 2nd Oct 2023 at 14:45

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