ERGA HiC Pri Scaffolding+QC YaHS v2505 (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 assembly (and alternate contigs) using YaHS. It also runs Pretext and all the QC analyses (gfastats, BUSCO, and Merqury).
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| (Trimmed) Hi-C Reads | (Trimmed) Hi-C Reads | Collection of Hi-C reads in fastq format |
|
| Alt (Purged) Contigs GFA | Alt (Purged) Contigs GFA | Alternate contigs in GFA format from the Purge_Dups run results: alt_purged_gfa |
|
| Estimated genome size | Estimated genome size | Select the est_genome_size result obtained during profiling |
|
| Lineage | Lineage | lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ... |
|
| Meryl database | Meryl database | Select the meryl_db result obtained during profiling |
|
| Multiple Hi-C paired-end files? | Multiple Hi-C paired-end files? | IMPORTANT! If you have more than one pair of paired-end files, select Yes |
|
| Pri (Purged) Contigs GFA | Pri (Purged) Contigs GFA | Primary contigs in GFA format from the Purge_Dups run results: pri_purged_gfa |
|
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+galaxy4 |
| 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+galaxy2 |
| 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/1.1.3+galaxy0 |
| 18 | Pairtools sort | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_sort/pairtools_sort/1.1.3+galaxy0 |
| 19 | Pairtools dedup | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_dedup/pairtools_dedup/1.1.3+galaxy0 |
| 20 | Pairtools split | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_split/pairtools_split/1.1.3+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/0.0.4+galaxy0 |
| 24 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 25 | Convert FASTA to fai file | CONVERTER_fasta_to_fai |
| 26 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy4 |
| 27 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
| 28 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
| 29 | Cut | Cut1 |
| 30 | Extract dataset | __EXTRACT_DATASET__ |
| 31 | Sambamba merge | toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_merge/sambamba_merge/1.0.1+galaxy2 |
| 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/1.1.3+galaxy0 |
| 35 | Pairtools sort | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_sort/pairtools_sort/1.1.3+galaxy0 |
| 36 | Pairtools dedup | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_dedup/pairtools_dedup/1.1.3+galaxy0 |
| 37 | Pairtools split | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_split/pairtools_split/1.1.3+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/0.0.4+galaxy0 |
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 |
|
| parsed_pairs_stats | parsed_pairs_stats | 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
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Version 1 (earliest) Created 24th Sep 2024 at 22:54 by Diego De Panis
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Views: 3911 Downloads: 799 Runs: 71
Created: 24th Sep 2024 at 22:54
Last updated: 1st Jun 2025 at 12:05
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ERGA Assembly Galax...
Biodiversity & ecol...
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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/
This is an inclusive collection of workflows related to biodiversity and ecology (especially non-microbial). A big portion covers genome assembly of newly-sequenced species, using long reads (ONT or PacBio HiFi), possibly complemented by chromosome capture (typically HiC) for scaffolding, or/and by short reads (typically Illumina). It also aims at collating workflows related to ecology, biodiversity, biogeography, natural history, and related scientific areas, across the whole WorkflowHub and ...
Maintainers: Matúš Kalaš, Keiler Collier
Number of items: 28
Tags: Biodiversity, Ecology, Genome assembly, dna barcoding, natural history collections
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. ...
