Simple COVID-19 - PE Variation 1.0
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Run on GalaxyAnalysis of variation within individual COVID-19 samples (Paired End Illumina). Does not use paured
Associated Tutorial
This workflows is part of the tutorial From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis, available in the GTN
Thanks to...
Tutorial Author(s): Marius van den Beek, Dave Clements, Daniel Blankenberg, Anton Nekrutenko
Tutorial Contributor(s): Wolfgang Maier, Saskia Hiltemann, Björn Grüning, Helena Rasche, Mélanie Petera, Nicola Soranzo, Anton Nekrutenko
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| NC_045512.2 fasta file | #main/NC_045512.2 fasta file | Contains SARS-CoV-2 reference sequence |
|
| SRA Manifest | #main/SRA Manifest | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Faster Download and Extract Reads in FASTQ | toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1 |
| 3 | fastp | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0 |
| 4 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
| 5 | MarkDuplicates | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 |
| 6 | Realign reads | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0 |
| 7 | Samtools stats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 |
| 8 | Insert indel qualities | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0 |
| 9 | Call variants | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0 |
| 10 | SnpEff eff: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19 |
| 11 | SnpSift Extract Fields | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 |
| 12 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| MultiQC Report PE | #main/MultiQC Report PE | n/a |
|
| Realigned Alignments with Indel Qualities | #main/Realigned Alignments with Indel Qualities | n/a |
|
| SnpSift tabular output | #main/SnpSift tabular output | n/a |
|
| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
Version History
master
Creators and Submitter
Views: 49 Downloads: 3 Runs: 0
Created: 2nd Jun 2025 at 11:02
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