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: 4613 Downloads: 768 Runs: 0
Created: 18th Jun 2020 at 00:03
Last updated: 1st Jul 2020 at 10:03
AttributionsNone
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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
