sars-cov-2-se-illumina-wgs-variant-calling/COVID-19-SE-WGS-ILLUMINA
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Run on GalaxyThis workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq
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 |
|
| Single End Collection | #main/Single End Collection | Illumina reads with fastqsanger encoding |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | fastp | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4 |
| 3 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 |
| 4 | MarkDuplicates | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0 |
| 5 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 |
| 6 | Realign reads | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0 |
| 7 | Insert indel qualities | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1 |
| 8 | Call variants | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3 |
| 9 | Lofreq filter | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0 |
| 10 | 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 |
|---|---|---|---|
| annotated_variants | #main/annotated_variants | n/a |
|
| annotated_variants_stats | #main/annotated_variants_stats | n/a |
|
| called_variant | #main/called_variant | n/a |
|
| fastp_html_report | #main/fastp_html_report | n/a |
|
| mapped_reads | #main/mapped_reads | n/a |
|
| markduplicates_reads | #main/markduplicates_reads | n/a |
|
| markduplicates_stats | #main/markduplicates_stats | n/a |
|
| preprocessed_reads | #main/preprocessed_reads | n/a |
|
| preprocessing_and_mapping_reports | #main/preprocessing_and_mapping_reports | n/a |
|
| realigned_deduplicated_mapped_reads | #main/realigned_deduplicated_mapped_reads | n/a |
|
| realigned_deduplicated_mapped_reads_with_indel_quals | #main/realigned_deduplicated_mapped_reads_with_indel_quals | n/a |
|
| soft_filtered_variants | #main/soft_filtered_variants | n/a |
|
Version History
v0.1.6 (latest) Created 26th Mar 2025 at 12:00 by WorkflowHub Bot
Updated to v0.1.6
Frozen
v0.1.6a9c7c09
v0.1 (earliest) Created 12th Mar 2021 at 13:41 by WorkflowHub Bot
Added/updated 8 files
Frozen
master6005b83
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Views: 11102 Downloads: 9362 Runs: 0
Created: 12th Mar 2021 at 13:41
Last updated: 18th Aug 2025 at 18:33
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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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Space: Galaxy
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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, ...
