Workflow Type: Galaxy
Open
Frozen
Assembly with preprocessing
Associated Tutorial
This workflows is part of the tutorial assembly_with_preprocessing, available in the GTN
Thanks to...
Tutorial Author(s): Wolfgang Maier
Inputs
ID | Name | Description | Type |
---|---|---|---|
Collection of long-reads data | Collection of long-reads data | n/a |
|
Collection of paired short-reads data | Collection of paired short-reads data | n/a |
|
Steps
ID | Name | Description |
---|---|---|
10 | Samtools fastx | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 |
11 | Samtools fastx | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 |
12 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
13 | Zip Collection | __ZIP_COLLECTION__ |
14 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
15 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
16 | seqtk_sample | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2 |
17 | seqtk_sample | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2 |
18 | Create assemblies with Unicycler | toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0 |
19 | Bandage Info | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1 |
2 | fastp: Trimmed Illumina Reads | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1 |
20 | Filter sequences by length | toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2 |
21 | Bandage Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2 |
3 | NanoPlot | toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1 |
4 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1 |
5 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 |
6 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0 |
7 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1 |
8 | Samtools stats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 |
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 |
|
_anonymous_output_4 | _anonymous_output_4 | n/a |
|
_anonymous_output_5 | _anonymous_output_5 | n/a |
|
_anonymous_output_6 | _anonymous_output_6 | n/a |
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_anonymous_output_7 | _anonymous_output_7 | n/a |
|
_anonymous_output_8 | _anonymous_output_8 | n/a |
|
_anonymous_output_9 | _anonymous_output_9 | n/a |
|
_anonymous_output_10 | _anonymous_output_10 | n/a |
|
_anonymous_output_11 | _anonymous_output_11 | n/a |
|
_anonymous_output_12 | _anonymous_output_12 | n/a |
|
_anonymous_output_13 | _anonymous_output_13 | n/a |
|
_anonymous_output_14 | _anonymous_output_14 | n/a |
|
_anonymous_output_15 | _anonymous_output_15 | n/a |
|
_anonymous_output_16 | _anonymous_output_16 | n/a |
|
_anonymous_output_17 | _anonymous_output_17 | n/a |
|
_anonymous_output_18 | _anonymous_output_18 | n/a |
|
Version History
1.0 (latest) Created 16th Jul 2024 at 14:09 by Helena Rasche
Added/updated 4 files
Open
master
b21be8f
2.0 (earliest) Created 25th Jun 2024 at 11:01 by Helena Rasche
Added/updated 4 files
Frozen
2.0
b9e8765
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
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Activity
Views: 203 Downloads: 84
Created: 25th Jun 2024 at 11:01
Last updated: 25th Jun 2024 at 11:01
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
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