Version 1

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 NC_045512.2 FASTA sequence of SARS-CoV-2 Fasta sequence for Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome
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Paired Collection Paired Collection Illumina reads with fastqsanger encoding
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ID Name Description
2 fastp
3 Map with BWA-MEM
4 Samtools view
5 MarkDuplicates
6 Samtools stats
7 Realign reads
8 MultiQC
9 Insert indel qualities
10 Call variants
11 Lofreq filter
12 SnpEff eff covid19 version


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

Version 1 (earliest) Created 1st Mar 2021 at 12:11 by WorkflowHub Sandbox Bot

Added/updated 8 files

Open master dc64be0
help Creators and Submitter
Not specified
Additional credit

Wolfgang Maier


Views: 1191   Downloads: 158

Created: 1st Mar 2021 at 12:11

help Attributions


Total size: 63.6 KB
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