sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA

Workflow Type: Galaxy

COVID-19: variation analysis on WGS PE data

This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.

Inputs

ID Name Description Type
NC_045512.2 FASTA sequence of SARS-CoV-2 #main/NC_045512.2 FASTA sequence of SARS-CoV-2 Fasta sequence for Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome
  • File
Paired Collection #main/Paired Collection Illumina reads with fastqsanger encoding
  • array containing
    • File

Steps

ID Name Description
2 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
3 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
4 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
5 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
6 MarkDuplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
7 Realign reads toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
8 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1
9 Insert indel qualities toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
10 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
11 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
12 SnpEff eff covid19 version toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19

Outputs

ID Name Description Type
Map with BWA-MEM on input dataset(s) (mapped reads in BAM format) #main/Map with BWA-MEM on input dataset(s) (mapped reads in BAM format) n/a
  • File
annotated_variants #main/annotated_variants n/a
  • File
annotated_variants_stats #main/annotated_variants_stats n/a
  • File
called_variants #main/called_variants n/a
  • File
fastp_html_report #main/fastp_html_report n/a
  • File
fastp_pe #main/fastp_pe n/a
  • File
filtered_mapped_reads #main/filtered_mapped_reads n/a
  • File
mapped_reads_stats #main/mapped_reads_stats n/a
  • File
markduplicates_reads #main/markduplicates_reads n/a
  • File
markduplicates_stats #main/markduplicates_stats n/a
  • File
preprocessing_and_mapping_reports #main/preprocessing_and_mapping_reports n/a
  • File
realigned_deduplicated_filtered_mapped_reads #main/realigned_deduplicated_filtered_mapped_reads n/a
  • File
realigned_deduplicated_filtered_mapped_reads_with_indel_quals #main/realigned_deduplicated_filtered_mapped_reads_with_indel_quals n/a
  • File
soft_filtered_variants #main/soft_filtered_variants n/a
  • File

Version History

Version 2 (latest) Created 30th Aug 2021 at 17:01 by Simone Leo

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Version 1 (earliest) Created 30th Aug 2021 at 17:00 by Simone Leo

No revision comments

help Creators and Submitter
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Additional credit

Wolfgang Maier

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Views: 630   Downloads: 10

Created: 30th Aug 2021 at 17:00

Last updated: 30th Aug 2021 at 17:01

Last used: 7th Dec 2022 at 01:12

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