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.
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 |
|
Single End Collection | Single End 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 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2 |
4 | MarkDuplicates | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 |
5 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1 |
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+galaxy0 |
8 | Call variants | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0 |
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 |
---|---|---|---|
preprocessed_reads | preprocessed_reads | n/a |
|
fastp_html_report | fastp_html_report | n/a |
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mapped_reads | mapped_reads | n/a |
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markduplicates_stats | markduplicates_stats | n/a |
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markduplicates_reads | markduplicates_reads | n/a |
|
preprocessing_and_mapping_reports | preprocessing_and_mapping_reports | n/a |
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realigned_deduplicated_mapped_reads | realigned_deduplicated_mapped_reads | n/a |
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realigned_deduplicated_mapped_reads_with_indel_quals | realigned_deduplicated_mapped_reads_with_indel_quals | n/a |
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called_variant | called_variant | n/a |
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soft_filtered_variants | soft_filtered_variants | n/a |
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annotated_variants | annotated_variants | n/a |
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annotated_variants_stats | annotated_variants_stats | n/a |
|
Version History
Version 2 (latest) Created 30th Aug 2021 at 17:01 by Simone Leo
No revision comments
Version 1 (earliest) Created 30th Aug 2021 at 17:00 by Simone Leo
No revision comments
Creators and Submitter
Creators
Not specifiedAdditional credit
Wolfgang Maier
Submitter
License
Activity
Views: 1957 Downloads: 446
Created: 30th Aug 2021 at 17:00
Last updated: 30th Aug 2021 at 17:01
Attributions
None