Scaffolding-HiC-VGP8/main
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Run on GalaxyThis workflow performs the scaffolding of a genome assembly using HiC data with YAHS. Can be used on any assembly with Hi-C data, and the assembly in the gfa format. You can generate a gfa from a fasta using the gfastat tool. Part of the VGP set of workflows, it is meant to be run after the contigging (workflows 3,4, or 5), optional purging step (Workflow 6 or 6b), and an optionnal scaffolding with Bionano data (Workflow 7). This workflow includes QC with Assembly statistics, Busco, and Hi-C maps.
Steps
| ID | Name | Description |
|---|---|---|
| 10 | Species Name: | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 11 | Assembly Name: | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 12 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 13 | Map parameter value | toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0 |
| 14 | Haplotype: | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 15 | Lineage used for Busco | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 16 | Parse parameter value | param_value_from_file |
| 17 | Trim and Align Hi-C paired collection | n/a |
| 18 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 19 | Samtools merge | toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2 |
| 20 | YAHS | toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2 |
| 21 | Hi-C Alignment Stats pre-scaffolding | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 |
| 22 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1 |
| 23 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0 |
| 24 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0 |
| 25 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 26 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 27 | Extract dataset | __EXTRACT_DATASET__ |
| 28 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 29 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 30 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
| 31 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy4 |
| 32 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
| 33 | compleasm | toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy2 |
| 34 | gfastats_data_prep | n/a |
| 35 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0 |
| 36 | Samtools merge | toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2 |
| 37 | Cut | Cut1 |
| 38 | Cut | Cut1 |
| 39 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1 |
| 40 | Hi-C Alignment Stats scaffolds | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 |
| 41 | Size Plot | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2 |
| 42 | Nx Plot | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2 |
| 43 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0 |
| 44 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 |
| 45 | Extract dataset | __EXTRACT_DATASET__ |
Version History
v0.1 (earliest) Created 27th Oct 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.195a269d
Creators and Submitter
Views: 11150 Downloads: 3254 Runs: 5
Created: 27th Oct 2023 at 03:01
Last updated: 29th May 2025 at 03:02
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Related items
IWC - Intergalactic Workflow Commission
Space: This Team is not associated with a Space
Public web page: https://github.com/galaxyproject/iwc
