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.


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


ID Name Description
2 fastp
3 Map with BWA-MEM
4 Samtools view
5 Samtools stats
6 MarkDuplicates
7 Realign reads
8 MultiQC
9 Insert indel qualities
10 Call variants
11 Lofreq filter
12 SnpEff eff covid19 version


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
Not specified
Additional credit

Wolfgang Maier


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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