ERGA Long Reads PriAlt Purge+QC v2505 (WF3)
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Run on GalaxyThe workflow takes a Long Reads collection, Pri/Alt contigs, and the values for transition parameter and max coverage depth (calculated from WF1) to run Purge_Dups. It produces purged Pri and Alt contigs assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury).
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| (Trimmed) Long Reads | (Trimmed) Long Reads | Collection of Long reads in fastq format |
|
| Alt Contigs GFA | Alt Contigs GFA | Alternate contigs in GFA format from the Hifiasm run results: alt_contigs_gfa |
|
| Estimated genome size | Estimated genome size | Select the est_genome_size result obtained during profiling |
|
| Meryl database | Meryl database | Select the meryl_db result obtained during profiling |
|
| Pri Contigs GFA | Pri Contigs GFA | Primary contigs in GFA format from the Hifiasm run results: pri_contigs_gfa |
|
| Transition parameter | Transition parameter | Select the transition_param result obtained during profiling |
|
| What type of Long Reads? | What type of Long Reads? | Select map-hifi if the long reads are PacBio HiFi (default), map-ont if the long reads are ONT |
|
| lineage | lineage | lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ... |
|
| max depth | max depth | Select the max_depth result obtained during profiling |
|
Steps
| ID | Name | Description |
|---|---|---|
| 9 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
| 10 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
| 11 | Parse parameter value | param_value_from_file |
| 12 | Parse parameter value | param_value_from_file |
| 13 | Parse parameter value | param_value_from_file |
| 14 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 15 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1 |
| 16 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1 |
| 17 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 18 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 19 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 20 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 21 | Concatenate datasets | cat1 |
| 22 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
| 23 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 24 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 25 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1 |
| 26 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1 |
| 27 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 28 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 29 | Purge overlaps | toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0 |
| 30 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
| 31 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 32 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 33 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
Version History
Version 2 (latest) Created 1st Jun 2025 at 12:24 by Diego De Panis
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Version 1 (earliest) Created 24th Sep 2024 at 22:44 by Diego De Panis
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Views: 2360 Downloads: 330 Runs: 53
Created: 24th Sep 2024 at 22:44
Last updated: 1st Jun 2025 at 12:25
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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
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 reads and Illumina 3-dimensional Chromatin Confirmation Capture (Hi-C) reads
Executing the workflows collection will output a scaffolded primary assembly and alternate contigs, with the complete QC analyses
Please run the workflows in order: WF0', WF1, WF2, WF3, WF4
'Notice there is one for HiFi, one for ONT, and one for Illumina (WGS or Hi-C). Run according to your data. ...
