Workflow Type: Galaxy
Open
Frozen
Stable
The workflow takes a long reads collection (HiFi, or ONT also possible now), and max coverage depth (calculated from WF1) to run Hifiasm in solo mode. It produces a Pri/Alt assembly, Bandage plots, and runs all the QC analysis (gfastats, BUSCO, and Merqury).
Inputs
ID | Name | Description | Type |
---|---|---|---|
(Trimmed) Long Reads Collection | #main/(Trimmed) Long Reads Collection | Collection of Long reads in fastq format |
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Estimated genome size | #main/Estimated genome size | Select the est_genome_size result obtained during profiling |
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Hifiasm level of dups purging | #main/Hifiasm level of dups purging | 0 to disable, 1 to only purge contained haplotigs, 2 to purge all types of haplotigs, 3 to purge all types of haplotigs in the most aggressive way. In default, 3 for non-trio assembly, 0 for trio-binning assembly. For trio-binning assembly, only level 0 and level 1 are allowed. |
|
Meryl Database | #main/Meryl Database | Select the meryl_db result obtained during profiling |
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The Long Reads are PacBio HiFi | #main/The Long Reads are PacBio HiFi | If your long reads are HiFi, leave it 'yes' |
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The Long reads are ONT | #main/The Long reads are ONT | If your long reads are ONT, switch to 'yes'. IMPORTANT: Remember to also switch HiFi to 'no' |
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lineage | #main/lineage | lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ... |
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max depth | #main/max depth | Select the max_depth result obtained during profiling |
|
Steps
ID | Name | Description |
---|---|---|
8 | Parse parameter value | param_value_from_file |
9 | Parse parameter value | param_value_from_file |
10 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0 |
11 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0 |
12 | Bandage Pri (HiFi) | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
13 | gfastats pri (HiFi) | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
14 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
15 | Bandage alt | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
16 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
17 | gfastats alt | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
18 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
19 | Bandage Pri (ONT) | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
20 | gfastats pri (ONT) | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
21 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
22 | Bandage alt (ONT) | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
23 | gfastats alt (ONT) | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
24 | BUSCO pri (HiFi) | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
25 | BUSCO alt (HiFi) | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
26 | Merqury pri/alt (HiFi) | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
27 | BUSCO pri (ONT) | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
28 | Merqury pri/alt (ONT) | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
29 | BUSCO alt (ONT) | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
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_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 |
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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
Version 2 (latest) Created 30th May 2025 at 13:52 by Diego De Panis
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Version 1 (earliest) Created 24th Sep 2024 at 22:29 by Diego De Panis
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Created: 24th Sep 2024 at 22:29
Last updated: 30th May 2025 at 13:55
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