Scaffolding-HiC-VGP8/main

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Workflow Type: Galaxy

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. 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.

SEEK ID: https://workflowhub.eu/workflows/625?version=25

Steps

ID Name Description
11 Species Name: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
12 Assembly Name: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
13 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
14 Map parameter value toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
15 Haplotype: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
16 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
17 Lineage used for Busco toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
18 Parse parameter value param_value_from_file
19 Trim and Align Hi-C paired collection n/a
20 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
21 Filter BAM toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy3
22 Test if collection has only one item or is empty n/a
23 Samtools merge toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0
24 Extract dataset __EXTRACT_DATASET__
25 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
26 YAHS toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2
27 Hi-C Alignment Stats pre-scaffolding toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.7
28 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
29 Hi-C Alignment Stats contigs summary toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.7
30 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2
31 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy0
32 Extract dataset __EXTRACT_DATASET__
33 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
34 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
35 Extract dataset __EXTRACT_DATASET__
36 Select last toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy2
37 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
38 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
39 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
40 Add Contigs headers toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2
41 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.3+galaxy0
42 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
43 compleasm toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy2
44 gfastats_data_prep n/a
45 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2
46 Filter BAM toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy3
47 Cut Cut1
48 Cut Cut1
49 Samtools merge toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0
50 Extract dataset __EXTRACT_DATASET__
51 Size Plot toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2
52 Nx Plot toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2
53 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
54 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
55 Hi-C Alignment Stats scaffolds toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.7
56 Hi-C Alignment Stats scaffolds summary toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.7
57 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy0
58 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3
59 Extract dataset __EXTRACT_DATASET__
60 Extract dataset __EXTRACT_DATASET__
61 Select last toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy2
62 Add Scaffolds header toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2
63 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy2
64 Merged Summary Stats toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy2

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help Creators and Submitter
Creators
Not specified
Additional credit

VGP, Galaxy

Submitter
Tools
gfastats
Bwa-mem2
BUSCO
ggplot2
SAMtools
Compleasm
MultiQC
BamTools
License
Creative Commons Attribution 4.0 International
Activity

Views: 16272   Downloads: 16319   Runs: 8

Created: 27th Oct 2023 at 03:01

Last updated: 31st Aug 2025 at 03:01

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