sars-cov-2-se-illumina-wgs-variant-calling/COVID-19-SE-WGS-ILLUMINA
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Tests 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 |
|
| mapped_reads | mapped_reads | n/a |
|
| markduplicates_stats | markduplicates_stats | n/a |
|
| markduplicates_reads | markduplicates_reads | n/a |
|
| preprocessing_and_mapping_reports | preprocessing_and_mapping_reports | n/a |
|
| realigned_deduplicated_mapped_reads | realigned_deduplicated_mapped_reads | n/a |
|
| realigned_deduplicated_mapped_reads_with_indel_quals | realigned_deduplicated_mapped_reads_with_indel_quals | n/a |
|
| called_variant | called_variant | 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
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
Views: 1253 Downloads: 183
Created: 30th Aug 2021 at 17:00
Last updated: 30th Aug 2021 at 17:01
AttributionsNone
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https://orcid.org/0000-0001-8271-5429
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