Unicycler assembly and annotation Version 1
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Run on GalaxyAlignment, assembly RNASEQ reads and annotation of generated transcripts.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| List of Illumina accessions | List of Illumina accessions | n/a |
|
| SARS-CoV-2 proteins | SARS-CoV-2 proteins | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | UniProt | toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.1.0 |
| 3 | Illumina data | toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4 |
| 4 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
| 5 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
| 6 | fastp: Trimmed Illumina Reads | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1 |
| 7 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
| 8 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 |
| 9 | Filter SAM or BAM, output SAM or BAM | toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1 |
| 10 | Illumina filtered reads | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 |
| 11 | MergeSamFiles | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1 |
| 12 | Illumina filtered and merged reads | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 |
| 13 | Unicycler assembly | toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0 |
| 14 | Glimmer ICM builder | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2 |
| 15 | Antismash | toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/4.1 |
| 16 | TransDecoder | toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1 |
| 17 | Glimmer3 | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2 |
| 18 | jackhmmer | toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_jackhmmer/0.1.0 |
| 19 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
| 20 | NCBI BLAST+ blastp | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 |
| 21 | NCBI BLAST+ blastp | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 |
| 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_3 | _anonymous_output_3 | n/a |
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| _anonymous_output_4 | _anonymous_output_4 | n/a |
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| _anonymous_output_5 | _anonymous_output_5 | n/a |
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| _anonymous_output_6 | _anonymous_output_6 | n/a |
|
| _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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| fastq | fastq | n/a |
|
| fast | fast | n/a |
|
| _anonymous_output_14 | _anonymous_output_14 | n/a |
|
| n/a | n/a | 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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| _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 |
|
Version History
Version 1 (earliest) Created 18th Jun 2020 at 00:07 by Ambarish Kumar
Added/updated 2 files
Open
master27e1a69
Creators and Submitter
Views: 6203 Downloads: 874 Runs: 4
Created: 18th Jun 2020 at 00:07
Last updated: 1st Jul 2020 at 10:00
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
