Assembly using Tophat2 and annotation (alternate) Version 1
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Run on GalaxyAlignment, assembly and annotation of RNQSEQ reads using TOPHAT (without filtering out host reads).
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| List of Illumina accessions | List of Illumina accessions | n/a |
|
| Reference annotation | Reference annotation | n/a |
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| Reference genome. | Reference genome. | n/a |
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| SARS-CoV-2 proteins | SARS-CoV-2 proteins | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | UniProt | toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.1.0 |
| 5 | Illumina data | toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4 |
| 6 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
| 7 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
| 8 | fastp: Trimmed Illumina Reads | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1 |
| 9 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 |
| 10 | TopHat | toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.1 |
| 11 | Cufflinks | toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.2 |
| 12 | Cuffmerge | toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.1 |
| 13 | gffread | toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2 |
| 14 | TransDecoder | toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1 |
| 15 | Antismash | toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/4.1 |
| 16 | Glimmer ICM builder | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2 |
| 17 | jackhmmer | toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_jackhmmer/0.1.0 |
| 18 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
| 19 | NCBI BLAST+ blastp | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 |
| 20 | NCBI BLAST+ blastp | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 |
| 21 | Glimmer3 | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2 |
| 22 | NCBI BLAST+ blastp | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
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| _anonymous_output_6 | _anonymous_output_6 | n/a |
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| _anonymous_output_7 | _anonymous_output_7 | n/a |
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| _anonymous_output_8 | _anonymous_output_8 | n/a |
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| _anonymous_output_9 | _anonymous_output_9 | n/a |
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| _anonymous_output_10 | _anonymous_output_10 | n/a |
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| _anonymous_output_11 | _anonymous_output_11 | n/a |
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| _anonymous_output_12 | _anonymous_output_12 | n/a |
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| _anonymous_output_13 | _anonymous_output_13 | n/a |
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| _anonymous_output_14 | _anonymous_output_14 | n/a |
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| _anonymous_output_15 | _anonymous_output_15 | n/a |
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| _anonymous_output_16 | _anonymous_output_16 | n/a |
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| _anonymous_output_17 | _anonymous_output_17 | n/a |
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| _anonymous_output_18 | _anonymous_output_18 | n/a |
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| _anonymous_output_19 | _anonymous_output_19 | n/a |
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| _anonymous_output_20 | _anonymous_output_20 | n/a |
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| _anonymous_output_21 | _anonymous_output_21 | n/a |
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| _anonymous_output_22 | _anonymous_output_22 | n/a |
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| _anonymous_output_23 | _anonymous_output_23 | n/a |
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| _anonymous_output_24 | _anonymous_output_24 | n/a |
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| fasta | fasta | n/a |
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| _anonymous_output_25 | _anonymous_output_25 | n/a |
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| _anonymous_output_26 | _anonymous_output_26 | n/a |
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| _anonymous_output_27 | _anonymous_output_27 | n/a |
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| _anonymous_output_28 | _anonymous_output_28 | n/a |
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| _anonymous_output_29 | _anonymous_output_29 | n/a |
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| _anonymous_output_30 | _anonymous_output_30 | n/a |
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| _anonymous_output_31 | _anonymous_output_31 | n/a |
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| _anonymous_output_32 | _anonymous_output_32 | n/a |
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| _anonymous_output_33 | _anonymous_output_33 | n/a |
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| _anonymous_output_34 | _anonymous_output_34 | n/a |
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| _anonymous_output_35 | _anonymous_output_35 | n/a |
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| _anonymous_output_36 | _anonymous_output_36 | n/a |
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| _anonymous_output_37 | _anonymous_output_37 | n/a |
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| _anonymous_output_38 | _anonymous_output_38 | n/a |
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| _anonymous_output_39 | _anonymous_output_39 | n/a |
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| _anonymous_output_40 | _anonymous_output_40 | n/a |
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| _anonymous_output_41 | _anonymous_output_41 | n/a |
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| _anonymous_output_42 | _anonymous_output_42 | n/a |
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| _anonymous_output_43 | _anonymous_output_43 | n/a |
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| _anonymous_output_44 | _anonymous_output_44 | n/a |
|
Version History
Version 1 (earliest) Created 18th Jun 2020 at 00:03 by Ambarish Kumar
Added/updated 2 files
Open
masterd64ffd6
Creators and Submitter
Views: 4626 Downloads: 773 Runs: 0
Created: 18th Jun 2020 at 00:03
Last updated: 1st Jul 2020 at 10:03
AttributionsNone
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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 ...
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Web page: https://github.com/virtual-biohackathons/covid-19-bh20
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Public web page: https://github.com/galaxyproject/SARS-CoV-2
