Scaffolding-HiC-VGP8/main
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Workflow Type: Galaxy
Frozen
This 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.
Steps
| ID | Name | Description |
|---|---|---|
| 11 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1 |
| 12 | Assembly Info | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 13 | Map parameter value | toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0 |
| 14 | Compose text parameter value | 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 | Compute read coverage | n/a |
| 17 | Parse parameter value | param_value_from_file |
| 18 | Trim, Align, deduplicate Hi-C - Scaffolding | n/a |
| 19 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 20 | Filter BAM | toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.3+galaxy0 |
| 21 | Hi-C Alignment Stats pre-scaffolding | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9 |
| 22 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0 |
| 23 | Hi-C Alignment Stats contigs summary | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9 |
| 24 | Test if collection has only one item or is empty | n/a |
| 25 | YAHS | toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy3 |
| 26 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy1 |
| 27 | Extract dataset | __EXTRACT_DATASET__ |
| 28 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3 |
| 29 | Extract dataset | __EXTRACT_DATASET__ |
| 30 | Select last | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy3 |
| 31 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1 |
| 32 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1 |
| 33 | Add Contigs headers | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 34 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1 |
| 35 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1 |
| 36 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1 |
| 37 | gfastats_data_prep | n/a |
| 38 | BWA-MEM2 indexer | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2_idx/2.3+galaxy0 |
| 39 | compleasm | toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3 |
| 40 | Compute sequence length | toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4 |
| 41 | Cut | Cut1 |
| 42 | Cut | Cut1 |
| 43 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.3+galaxy0 |
| 44 | Cut | Cut1 |
| 45 | Size Plot | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2 |
| 46 | Nx Plot | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2 |
| 47 | Samtools merge | toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.22+galaxy1 |
| 48 | Extract dataset | __EXTRACT_DATASET__ |
| 49 | Image Montage | toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy1 |
| 50 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 51 | Samtools sort | toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.8 |
| 52 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0 |
| 53 | Hi-C Alignment Stats scaffolds | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9 |
| 54 | Hi-C Alignment Stats scaffolds summary | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9 |
| 55 | Pairtools parse | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_parse/pairtools_parse/1.1.3+galaxy6 |
| 56 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy1 |
| 57 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0 |
| 58 | Extract dataset | __EXTRACT_DATASET__ |
| 59 | Pairtools dedup | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_dedup/pairtools_dedup/1.1.3+galaxy6 |
| 60 | Extract dataset | __EXTRACT_DATASET__ |
| 61 | Alignment Scores | __EXTRACT_DATASET__ |
| 62 | Alignment Stats | __EXTRACT_DATASET__ |
| 63 | Select last | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy3 |
| 64 | Trim | trimmer |
| 65 | Image Montage | toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy1 |
| 66 | Add Scaffolds header | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 67 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0 |
| 68 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy3 |
| 69 | Parse pairtools merqury output | n/a |
| 70 | Merged Summary Stats | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy3 |
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
Activity
Views: 27352 Downloads: 148741 Runs: 10
Created: 27th Oct 2023 at 03:01
Last updated: 12th Mar 2026 at 03:01
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Scientific disciplines
Computer Science
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