workflow-generate-dataset-for-assembly-tutorial 1.0
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This workflows is part of the tutorial Assembly of metagenomic sequencing data, available in the GTN
Thanks to...
Tutorial Author(s): Polina Polunina, Bérénice Batut
Tutorial Contributor(s): Bérénice Batut, Saskia Hiltemann, Polina Polunina, Helena Rasche
Grants(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| ERR2231567_1.fastq.gz | #main/ERR2231567_1.fastq.gz | n/a |
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| ERR2231567_2.fastq.gz | #main/ERR2231567_2.fastq.gz | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0 |
| 3 | MEGAHIT | toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0 |
| 4 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1 |
| 5 | BAM filter | toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9 |
| 6 | BAM filter | toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9 |
| 7 | Convert, Merge, Randomize | toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0 |
| 8 | Convert, Merge, Randomize | toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0 |
| 9 | Select random lines | random_lines1 |
| 10 | Select random lines | random_lines1 |
| 11 | Filter Tabular | toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0 |
| 12 | Filter Tabular | toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0 |
| 13 | Unique | toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3 |
| 14 | Unique | toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3 |
| 15 | Concatenate datasets | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 |
| 16 | seqtk_subseq | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1 |
| 17 | seqtk_subseq | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1 |
| 18 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 19 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_10 | #main/_anonymous_output_10 | n/a |
|
| _anonymous_output_11 | #main/_anonymous_output_11 | n/a |
|
| _anonymous_output_12 | #main/_anonymous_output_12 | n/a |
|
| _anonymous_output_13 | #main/_anonymous_output_13 | n/a |
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| _anonymous_output_14 | #main/_anonymous_output_14 | n/a |
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| _anonymous_output_15 | #main/_anonymous_output_15 | n/a |
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| _anonymous_output_16 | #main/_anonymous_output_16 | n/a |
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| _anonymous_output_17 | #main/_anonymous_output_17 | n/a |
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| _anonymous_output_18 | #main/_anonymous_output_18 | n/a |
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| _anonymous_output_19 | #main/_anonymous_output_19 | n/a |
|
| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
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| _anonymous_output_20 | #main/_anonymous_output_20 | n/a |
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| _anonymous_output_21 | #main/_anonymous_output_21 | n/a |
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| _anonymous_output_22 | #main/_anonymous_output_22 | n/a |
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| _anonymous_output_23 | #main/_anonymous_output_23 | n/a |
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| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
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| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
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| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
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| _anonymous_output_6 | #main/_anonymous_output_6 | n/a |
|
| _anonymous_output_7 | #main/_anonymous_output_7 | n/a |
|
| _anonymous_output_8 | #main/_anonymous_output_8 | n/a |
|
| _anonymous_output_9 | #main/_anonymous_output_9 | n/a |
|
Version History
master
Creators and Submitter
Views: 1056 Downloads: 154 Runs: 0
Created: 2nd Jun 2025 at 10:55
AttributionsNone
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