Scaffolding-HiC-VGP8/main

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Workflow Type: Galaxy

This workflow perform the scaffolding of a genome assemble using HiC data with YAHS. Part of the VGP set of workflows.

SEEK ID: https://workflowhub.eu/workflows/625?version=18

Steps

ID Name Description
8 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
9 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
10 Parse parameter value param_value_from_file
11 Trim and Align Hi-C paired collection n/a
12 YAHS toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2
13 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
14 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
15 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0
16 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
17 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
18 Extract dataset __EXTRACT_DATASET__
19 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
20 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
21 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
22 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy4
23 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0
24 gfastats_data_prep n/a
25 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
26 Samtools merge toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2
27 Cut Cut1
28 Cut Cut1
29 bedtools BAM to BED toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0
30 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
31 Nx Plot toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1
32 Size Plot toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1
33 Sort toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy0
34 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0
35 Extract dataset __EXTRACT_DATASET__

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v3.5 (latest) Created 2nd Apr 2026 at 03:01 by WorkflowHub Bot

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help Creators and Submitter
Creators
Not specified
Additional credit

VGP, Galaxy

Submitter
Tools
gfastats
Bwa-mem2
ggplot2
SAMtools
Compleasm
MultiQC
BamTools
compute_sequence_length
License
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Activity

Views: 27346   Downloads: 148741   Runs: 10

Created: 27th Oct 2023 at 03:01

Last updated: 12th Mar 2026 at 03:01

Annotated Properties
Scientific disciplines
Computer Science
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