ERGA HiC Pri Scaffolding+QC YaHS v2501 (WF4)
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Run on GalaxyThe workflow takes trimmed HiC paired-end reads collection, and Pri/Alt assemblies to produce a scaffolded primary assembliy (and alternate contigs) using YaHS. It also runs all the QC analyses (gfastats, BUSCO, and Merqury).
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Alt GFA | Alt GFA | gfa assembly file of the Alt purged |
|
| Estimated genome size | Estimated genome size | n/a |
|
| HiC trimmed | HiC trimmed | n/a |
|
| Meryl database | Meryl database | n/a |
|
| Multiple HiC paired-end files? | Multiple HiC paired-end files? | IMPORTANT! If you have more than one pair of paired-end files, select Yes |
|
| Pri GFA | Pri GFA | gfa assembly file of the Pri purged to scaffold |
|
| lineage | lineage | lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ... |
|
Steps
| ID | Name | Description |
|---|---|---|
| 7 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
| 8 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
| 9 | Parse parameter value | param_value_from_file |
| 10 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
| 11 | Convert FASTA to fai file | CONVERTER_fasta_to_fai |
| 12 | Extract dataset | __EXTRACT_DATASET__ |
| 13 | Sambamba merge | toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_merge/sambamba_merge/1.0.1+galaxy1 |
| 14 | Cut | Cut1 |
| 15 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 16 | Sambamba flagstat | toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_flagstat/sambamba_flagstat/1.0.1+galaxy1 |
| 17 | Pairtools parse | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_parse/pairtools_parse/1.1.2+galaxy0 |
| 18 | Pairtools sort | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_sort/pairtools_sort/1.1.2+galaxy0 |
| 19 | Pairtools dedup | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_dedup/pairtools_dedup/1.1.2+galaxy0 |
| 20 | Pairtools split | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_split/pairtools_split/1.1.2+galaxy0 |
| 21 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1 |
| 22 | YAHS | toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2 |
| 23 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2 |
| 24 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
| 25 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 26 | Convert FASTA to fai file | CONVERTER_fasta_to_fai |
| 27 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0 |
| 28 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
| 29 | Extract dataset | __EXTRACT_DATASET__ |
| 30 | Sambamba merge | toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_merge/sambamba_merge/1.0.1+galaxy1 |
| 31 | Cut | Cut1 |
| 32 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 33 | Sambamba flagstat | toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_flagstat/sambamba_flagstat/1.0.1+galaxy1 |
| 34 | Pairtools parse | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_parse/pairtools_parse/1.1.2+galaxy0 |
| 35 | Pairtools sort | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_sort/pairtools_sort/1.1.2+galaxy0 |
| 36 | Pairtools dedup | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_dedup/pairtools_dedup/1.1.2+galaxy0 |
| 37 | Pairtools split | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_split/pairtools_split/1.1.2+galaxy0 |
| 38 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1 |
| 39 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | _anonymous_output_1 | n/a |
|
| _anonymous_output_2 | _anonymous_output_2 | n/a |
|
| _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 |
|
| dedup_pairs_stats | dedup_pairs_stats | n/a |
|
Version History
Version 2 (latest) Created 3rd Feb 2025 at 13:07 by Diego De Panis
Open
master1754422
Version 1 (earliest) Created 24th Sep 2024 at 22:54 by Diego De Panis
Initial commit
Frozen
Version-18a34969
Creators and SubmitterViews: 1124 Downloads: 115 Runs: 41
Created: 24th Sep 2024 at 22:54
Last updated: 3rd Feb 2025 at 13:12
AttributionsNone
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Teams: ERGA Assembly
Organizations: IZW
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 reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output a scaffolded primary assembliy and alternate contigs, with the complete QC analyses
Please run the workflows in order: WF0 (there are two, one for HiFi and one for Illumina HiC), WF1, WF2, WF3, WF4
