COVID-19: VARSCAN Version 1
Visit source
Download RO-Crate
Run on GalaxyDetects SNPs and INDELs using VARSCAN2.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| List of Illumina accessions | List of Illumina accessions | n/a |
|
| Reference genome | Reference genome | n/a |
|
| Reference genome annotation | Reference genome annotation | COVID-19 |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Illumina data | toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4 |
| 4 | SnpEff build: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4 |
| 5 | fastp: Trimmed Illumina Reads | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1 |
| 6 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 |
| 7 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
| 8 | Filter SAM or BAM, output SAM or BAM | toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1 |
| 9 | Illumina filtered reads | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 |
| 10 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0 |
| 11 | Samtools sort | toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3 |
| 12 | samtools mpileup | toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4 |
| 13 | VarScan mpileup | toolshed.g2.bx.psu.edu/repos/iuc/varscan_mpileup/varscan_mpileup/2.4.3.1 |
| 14 | VarScan mpileup | toolshed.g2.bx.psu.edu/repos/iuc/varscan_mpileup/varscan_mpileup/2.4.3.1 |
| 15 | VcfAllelicPrimitives: | toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0 |
| 16 | VcfAllelicPrimitives: | toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0 |
| 17 | SnpEff eff: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 |
| 18 | SnpEff eff: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 |
| 19 | SnpSift Extract Fields | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 |
| 20 | SnpSift Extract Fields | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 |
| 21 | Concatenate datasets | cat1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
|
| _anonymous_output_5 | _anonymous_output_5 | n/a |
|
| _anonymous_output_6 | _anonymous_output_6 | n/a |
|
| _anonymous_output_7 | _anonymous_output_7 | n/a |
|
| _anonymous_output_8 | _anonymous_output_8 | n/a |
|
| _anonymous_output_9 | _anonymous_output_9 | n/a |
|
| _anonymous_output_10 | _anonymous_output_10 | n/a |
|
| _anonymous_output_11 | _anonymous_output_11 | n/a |
|
| _anonymous_output_12 | _anonymous_output_12 | n/a |
|
| _anonymous_output_13 | _anonymous_output_13 | n/a |
|
| _anonymous_output_14 | _anonymous_output_14 | n/a |
|
| _anonymous_output_15 | _anonymous_output_15 | n/a |
|
| _anonymous_output_16 | _anonymous_output_16 | n/a |
|
| _anonymous_output_17 | _anonymous_output_17 | n/a |
|
| _anonymous_output_18 | _anonymous_output_18 | n/a |
|
| _anonymous_output_19 | _anonymous_output_19 | n/a |
|
| _anonymous_output_20 | _anonymous_output_20 | n/a |
|
| _anonymous_output_21 | _anonymous_output_21 | n/a |
|
| _anonymous_output_22 | _anonymous_output_22 | n/a |
|
| _anonymous_output_23 | _anonymous_output_23 | n/a |
|
| _anonymous_output_24 | _anonymous_output_24 | n/a |
|
| _anonymous_output_25 | _anonymous_output_25 | n/a |
|
| _anonymous_output_26 | _anonymous_output_26 | n/a |
|
| _anonymous_output_27 | _anonymous_output_27 | n/a |
|
| _anonymous_output_28 | _anonymous_output_28 | n/a |
|
| _anonymous_output_29 | _anonymous_output_29 | n/a |
|
Version History
Version 1 (earliest) Created 18th Jun 2020 at 23:57 by Ambarish Kumar
Added/updated 2 files
Open
masterde69d64
Creators and Submitter
Views: 5011 Downloads: 411 Runs: 0
Created: 18th Jun 2020 at 23:57
AttributionsNone
Related items
The goal of COVID-19-Biohackathon 2020 (COVID-19-BH20) is to develop and gather computational tools that can be useful for studying the biology of the virus and the disease.
The COVID-19 Programme in Workflow Hub aims to gather workflows for the analysis of COVID-19 molecular biology data and their metadata. In this programme, all workflows and their metadata will be curated and made interoperable, reusable and reproducible. All workflows and their metadata will be easily accessible to everyone ...
Teams: Connor Lab, GalaxyProject SARS-CoV-2, InSaFLU, nf-core viralrecon, CWL workflow SARS-CoV-2, V-Pipe, Test team
Web page: https://github.com/virtual-biohackathons/covid-19-bh20
Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures https://covid19.galaxyproject.org
Space: COVID-19 Biohackathon
Public web page: https://github.com/galaxyproject/SARS-CoV-2
