ERGA Long reads+HiC Assembly+QC Hifiasm v2602 (WF2)
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Run on GalaxyThe workflow takes a trimmed long reads collection, and Forward/Reverse HiC reads to run Hifiasm in HiC phasing mode. It produces both Pri/Alt and Hap1/Hap2 assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury). The default Hifiasm purge level is aggressive (l3).
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Estimated genome size | #main/Estimated genome size | n/a |
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| HiC F trimmed | #main/HiC F trimmed | n/a |
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| HiC R trimmed | #main/HiC R trimmed | n/a |
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| Meryl Database | #main/Meryl Database | n/a |
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| Trimmed HiFi Reads Collection | #main/Trimmed HiFi Reads Collection | Collection of Long reads in fastq format. |
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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 | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 7 | Parse parameter value | param_value_from_file |
| 8 | Parse parameter value | param_value_from_file |
| 9 | Hifiasm | toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.5+galaxy0 |
| 10 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
| 11 | Bandage Pri | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 12 | gfastats pri | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.5+galaxy0 |
| 13 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
| 14 | Bandage alt | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 15 | gfastats alt | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 16 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
| 17 | gfastats hap1 | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 18 | Bandage hap1 | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 19 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
| 20 | gfastats hap2 | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.5+galaxy0 |
| 21 | Bandage Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 22 | BUSCO pri | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0 |
| 23 | BUSCO alt | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0 |
| 24 | Merqury pri/alt | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2 |
| 25 | BUSCO hap1 | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0 |
| 26 | BUSCO hap2 | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0 |
| 27 | Merqury hap1/hap2 | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2 |
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_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 11th Feb 2026 at 20:03 by Diego De Panis
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master63c4f4b
Version 1 (earliest) Created 9th Oct 2023 at 13:47 by Diego De Panis
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Version-1958e932
Creators and Submitter
Views: 8415 Downloads: 764 Runs: 13
Created: 9th Oct 2023 at 13:47
Last updated: 11th Feb 2026 at 20:05
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ERGA Assembly Galax...
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https://orcid.org/0000-0002-3679-9585
Welcome to the ERGA Space!
Here we collect, curate and develop pipelines to assemble and annotation reference-quality genomes for all eukaryotic life.
For Genome Assembly pipelines head to our Assembly Team
For Genome Annotation pipelines head to our Annotation Team
Development, discussions and issue tracking takes place in the ERGA github repo
If you would like to join ...
Teams: ERGA Assembly, ERGA Annotation, ERGA Analysis, ERGA Sampling and Sample Processing
Web page: https://www.erga-biodiversity.eu/
A collection of workflows and pipelines developed as part of the ERGA consortium
Space: ERGA
Public web page: https://www.erga-biodiversity.eu/
Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be PacBio HiFi or ONT long reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output two scaffolded haplotype assemblies and the complete QC analyses
Please run the workflows in order: WF0 (there are for long reads and for Illumina HiC), WF1, WF2, WF3 (optional), WF4
Maintainers: Tom Brown, Diego De Panis
Number of items: 6
Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, HiFi, Hi-C, ONT
