VVV2_align

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

IMPORTANT:

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

Name

Description

Type

Ploidy file (Y for happloid)

n/a

Steps

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/0.7.12.1
5	bcftools mpileup	toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.4.0.0
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

Outputs

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

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

Open master a3c888c

VVV2_align_SE
Version 1