Chloroplast-genome-assembly-and-annotation 3.0
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Download RO-Crate
Run on GalaxyAssembly
Associated Tutorial
This workflows is part of the tutorial Chloroplast genome assembly, available in the GTN
Thanks to...
Tutorial Author(s): Anna Syme
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Illumina_reads | #main/Illumina_reads | n/a |
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| Nanopore_reads | #main/Nanopore_reads | n/a |
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| Tiny_set_illumina_read | #main/Tiny_set_illumina_read | n/a |
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| Tiny_set_nanopore_reads | #main/Tiny_set_nanopore_reads | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Flye assembly | toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6 |
| 5 | NanoPlot | toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1 |
| 6 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
| 7 | Fasta Statistics | toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0 |
| 8 | Bandage Info | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1 |
| 9 | Bandage Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2 |
| 10 | pilon | toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1 |
| 11 | Fasta Statistics | toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0 |
| 12 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
| 13 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
| 14 | Prokka | toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5 |
| 15 | JBrowse | toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0 |
| 16 | JBrowse | toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
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| _anonymous_output_10 | #main/_anonymous_output_10 | n/a |
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| _anonymous_output_11 | #main/_anonymous_output_11 | n/a |
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| _anonymous_output_12 | #main/_anonymous_output_12 | n/a |
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| _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 |
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| _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_24 | #main/_anonymous_output_24 | n/a |
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| _anonymous_output_25 | #main/_anonymous_output_25 | n/a |
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| _anonymous_output_26 | #main/_anonymous_output_26 | n/a |
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| _anonymous_output_27 | #main/_anonymous_output_27 | n/a |
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| _anonymous_output_28 | #main/_anonymous_output_28 | n/a |
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| _anonymous_output_29 | #main/_anonymous_output_29 | n/a |
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| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
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| _anonymous_output_30 | #main/_anonymous_output_30 | n/a |
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| _anonymous_output_31 | #main/_anonymous_output_31 | n/a |
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| _anonymous_output_32 | #main/_anonymous_output_32 | n/a |
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| _anonymous_output_33 | #main/_anonymous_output_33 | 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 |
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| _anonymous_output_7 | #main/_anonymous_output_7 | n/a |
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| _anonymous_output_8 | #main/_anonymous_output_8 | n/a |
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| _anonymous_output_9 | #main/_anonymous_output_9 | n/a |
|
Version History
master
Creators and Submitter
Views: 1169 Downloads: 155 Runs: 4
Created: 2nd Jun 2025 at 11:01
AttributionsNone
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Teams: Galaxy Training Network
Organizations: Galaxy
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