VVV2_align_SE Version 2
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Run on GalaxySINGLE-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).
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Ploidy file (Y for happloid) | 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 |
|
| _anonymous_output_3 | _anonymous_output_3 | n/a |
|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
|
| _anonymous_output_5 | _anonymous_output_5 | n/a |
|
| _anonymous_output_6 | _anonymous_output_6 | n/a |
|
| _anonymous_output_7 | _anonymous_output_7 | n/a |
|
| _anonymous_output_8 | _anonymous_output_8 | n/a |
|
| _anonymous_output_9 | _anonymous_output_9 | n/a |
|
| _anonymous_output_10 | _anonymous_output_10 | n/a |
|
| _anonymous_output_11 | _anonymous_output_11 | n/a |
|
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)
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Created: 27th Jun 2023 at 15:41
Last updated: 2nd Oct 2023 at 14:32
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