sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA
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Run on GalaxyCOVID-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 | NC_045512.2 FASTA sequence of SARS-CoV-2 | Fasta sequence for Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome |
|
| Paired Collection | Paired Collection | Illumina reads with fastqsanger encoding |
|
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 |
|---|---|---|---|
| fastp_pe | fastp_pe | n/a |
|
| fastp_html_report | fastp_html_report | n/a |
|
| 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 |
|
| filtered_mapped_reads | filtered_mapped_reads | n/a |
|
| mapped_reads_stats | mapped_reads_stats | n/a |
|
| markduplicates_stats | markduplicates_stats | n/a |
|
| markduplicates_reads | markduplicates_reads | n/a |
|
| realigned_deduplicated_filtered_mapped_reads | realigned_deduplicated_filtered_mapped_reads | n/a |
|
| preprocessing_and_mapping_reports | preprocessing_and_mapping_reports | n/a |
|
| realigned_deduplicated_filtered_mapped_reads_with_indel_quals | realigned_deduplicated_filtered_mapped_reads_with_indel_quals | n/a |
|
| called_variants | called_variants | n/a |
|
| soft_filtered_variants | soft_filtered_variants | n/a |
|
| annotated_variants | annotated_variants | n/a |
|
| annotated_variants_stats | annotated_variants_stats | n/a |
|
Version History
v0.2.2 (latest) Created 21st Dec 2021 at 03:01 by WorkflowHub Bot
Updated to v0.2.2
Open
master7df401a
v0.1 (earliest) Created 12th Mar 2021 at 13:41 by WorkflowHub Bot
Added/updated 8 files
Frozen
master
cff7a1e
Creators and Submitter
Views: 12289 Downloads: 5504 Runs: 4
Created: 12th Mar 2021 at 13:41
Last updated: 19th Aug 2025 at 09:46
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Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, nf-core
Organizations: Bots, European Galaxy Team
https://orcid.org/0000-0002-9464-6640
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
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Workflows developed by or used by BY-COVID project.
The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data. Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, ...
