Workflow to detect SNV from Illumina sequenced baculovirus isolates
1.0

Workflow Type: Galaxy

This standard workflow determines SNV positions from baculovirus isolates using bcftools.

Associated Tutorial

This workflows is part of the tutorial Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates, available in the GTN

Features

Thanks to...

Workflow Author(s): Jörg T. Wennmann

Tutorial Author(s): Jörg Wennmann

gtn star logo followed by the word workflows

Steps

ID Name Description
0 Download reference genome in FASTA format from NCBI Exactly one reference genome. toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0
1 Paired dataset collection in FASTQ format (downloaded from NCBI SRA) Provide a dataset list of paired (forward and reverse) reads in fastq format. toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1
2 Collapse Genbank file NCBI Download accepts multiple accession numbers and creates a list as output. Therefore, the Fasta files can contain multiple records. For this analysis just one reference genome is required and the list needs to be converted into one file. toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
3 Trim Galore! toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0
4 Rename reference genome sequence header Provide a descriptive and unique name for the reference sequence. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1
5 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18
6 bcftools mpileup toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4
7 bcftools call toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5
8 VCF Transformation The VCF is converted to an easier to read table format. toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc1+galaxy0
9 Relative allele frequency calculation The DPR value is further decomposed for each position and isolate and attached to the table. Four additional columns are added to the table: ALLELE, DPR.ALLELE, REL.ALT and REL.ALT.0.05. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
10 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1
11 Reduce dataset to ALT1 In this step the dataset is reduced to the first alternative nucleotide (ALT1) only. Filter1
12 SNV plot A general overview to access the isolates overall heterogeneity/homogeneity. toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1
13 SNV specificity calculation The DPR value is further decomposed for each position and sample and attached to the table. Four additional columns are added to the table: ALLELE, DPR.ALLELE, REL.ALT and REL.ALT.0.05. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
14 Filter Filter1
15 Filter Filter1
16 Filter Filter1
17 ggplot2 V15 dotplot Creates a ggplot2 SNV plot for each SNV specificity. toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1
18 ggplot2 CpGV-S dotplot Creates a ggplot2 SNV plot for each SNV specificity. toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1
19 ggplot2 CpGV-E2 dotplot Creates a ggplot2 SNV plot for each SNV specificity. toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1

Outputs

ID Name Description Type
bcftools_call_output bcftools_call_output n/a
  • File
vcf_table vcf_table n/a
  • File
vcf_table_ALT1 vcf_table_ALT1 n/a
  • File
vcf_table_ALT1_specificity vcf_table_ALT1_specificity n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 11:01 by GTN Bot

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Created: 2nd Jun 2025 at 11:01

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