Workflow Type: Galaxy

COVID-19: variation analysis on WGS SE data

This workflows performs single end read mapping with bowtie2 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 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
Single End Collection Single End Collection Illumina reads with fastqsanger encoding
  • File[]


ID Name Description
2 fastp
3 Bowtie2
4 MarkDuplicates
5 MultiQC
6 Realign reads
7 Insert indel qualities
8 Call variants
9 Lofreq filter
10 SnpEff eff covid19 version


ID Name Description Type
preprocessed_reads preprocessed_reads n/a
  • File
fastp_html_report fastp_html_report n/a
  • File
mapped_reads mapped_reads n/a
  • File
markduplicates_stats markduplicates_stats n/a
  • File
markduplicates_reads markduplicates_reads n/a
  • File
preprocessing_and_mapping_reports preprocessing_and_mapping_reports n/a
  • File
realigned_deduplicated_mapped_reads realigned_deduplicated_mapped_reads n/a
  • File
realigned_deduplicated_mapped_reads_with_indel_quals realigned_deduplicated_mapped_reads_with_indel_quals n/a
  • File
called_variant called_variant n/a
  • File
soft_filtered_variants soft_filtered_variants n/a
  • File
annotated_variants annotated_variants n/a
  • File
annotated_variants_stats annotated_variants_stats 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: 1347   Downloads: 213

Created: 30th Aug 2021 at 17:00

Last updated: 30th Aug 2021 at 17:01

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