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.

SEEK ID: https://workflowhub.eu/workflows/625?version=27

Steps

ID Name Description
11 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
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 and Align Hi-C paired collection n/a
19 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
20 Test if collection has only one item or is empty n/a
21 Samtools merge toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0
22 Extract dataset __EXTRACT_DATASET__
23 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
24 MarkDuplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0
25 Hi-C Alignment Stats pre-scaffolding toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.7
26 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
27 Hi-C Alignment Stats contigs summary toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.7
28 Filter BAM toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy3
29 Deduplication Summary toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2
30 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy0
31 Extract dataset __EXTRACT_DATASET__
32 YAHS toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy3
33 Select last Show tail1
34 Extract dataset __EXTRACT_DATASET__
35 Select last toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy2
36 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2
37 Add Contigs headers toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2
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 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
41 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
42 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
43 gfastats_data_prep n/a
44 BWA-MEM2 indexer toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2_idx/2.3+galaxy0
45 compleasm toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3
46 Compute sequence length toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4
47 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2
48 Cut Cut1
49 Cut Cut1
50 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.3+galaxy0
51 Select last toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy2
52 Cut Cut1
53 Nx Plot toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2
54 Size Plot toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2
55 Samtools merge toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0
56 Extract dataset __EXTRACT_DATASET__
57 Image Montage toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy0
58 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
59 Samtools sort toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.7
60 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
61 Hi-C Alignment Stats scaffolds toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.7
62 Hi-C Alignment Stats scaffolds summary toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.7
63 Pairtools parse toolshed.g2.bx.psu.edu/repos/iuc/pairtools_parse/pairtools_parse/1.1.3+galaxy6
64 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy0
65 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3
66 Extract dataset __EXTRACT_DATASET__
67 Pairtools dedup toolshed.g2.bx.psu.edu/repos/iuc/pairtools_dedup/pairtools_dedup/1.1.3+galaxy6
68 Extract dataset __EXTRACT_DATASET__
69 Select last toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy2
70 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3
71 Image Montage toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy0
72 Add Scaffolds header toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2
73 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy2
74 Merged Summary Stats toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy2
75 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2

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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
Activity

Views: 17970   Downloads: 27156   Runs: 9

Created: 27th Oct 2023 at 03:01

Last updated: 8th Oct 2025 at 03:01

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