assembly_with_preprocessing_and_sra_download 1.0
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Download RO-Crate
Run on GalaxyAssembly with preprocessing and SRA download
Associated Tutorial
This workflows is part of the tutorial Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads, available in the GTN
Thanks to...
Tutorial Author(s): Wolfgang Maier
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| List of Illumina accessions | List of Illumina accessions | n/a |
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| List of ONT accessions | List of ONT accessions | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 10 | Samtools stats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 |
| 11 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1 |
| 12 | Samtools fastx | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 |
| 13 | Samtools fastx | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 |
| 14 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
| 15 | Zip Collection | __ZIP_COLLECTION__ |
| 16 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
| 17 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
| 18 | seqtk_sample | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2 |
| 19 | seqtk_sample | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2 |
| 2 | Illumina data | toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1 |
| 20 | Create assemblies with Unicycler | toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0 |
| 21 | Bandage Info | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1 |
| 22 | Bandage Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2 |
| 23 | Filter sequences by length | toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2 |
| 3 | ONT data | toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1 |
| 4 | fastp: Trimmed Illumina Reads | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1 |
| 5 | NanoPlot | toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1 |
| 6 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1 |
| 7 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 |
| 8 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0 |
| 9 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1 |
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 |
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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 |
|
Version History
master
Creators and Submitter
Views: 1191 Downloads: 161 Runs: 4
Created: 2nd Jun 2025 at 11:01
AttributionsNone
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