hi-c-contact-map-for-assembly-manual-curation/main

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Workflow Type: Galaxy

This workflow generates Hi-C contact maps for genome assemblies in the Pretext format. It is compatible with one or 2 haplotypes. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies.

SEEK ID: https://workflowhub.eu/workflows/1327?version=6

Steps

ID Name Description
10 Hap2 not provided toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
11 Add suffix to 2 haplotypes n/a
12 concatenate HiFi toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1
13 Add Suffix 1 haplotype n/a
14 Pick Assembly toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
15 Trim and Align Hi-C paired collection n/a
16 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2
17 seqtk_telo toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0
18 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0
19 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
20 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
21 Cut Cut1
22 bamCoverage toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0
23 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
24 Add Coverage Track toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0
25 Test if telomere track is empty param_value_from_file
26 False if telomere track is empty toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
27 Add telomere track toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0
28 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
29 Add gaps track toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0
30 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0
31 Extract dataset __EXTRACT_DATASET__

Version History

v1.0beta6 (latest) Created 12th Jun 2025 at 03:01 by WorkflowHub Bot

Updated to v1.0beta6


Frozen v1.0beta6 5b4be3e

v1.0beta5 Created 15th May 2025 at 03:03 by WorkflowHub Bot

Updated to v1.0beta5


Frozen v1.0beta5 29022b1

v1.0beta4 Created 9th Apr 2025 at 03:01 by WorkflowHub Bot

Updated to v1.0beta4


Frozen v1.0beta4 942f789

v1.0beta3 Created 8th Apr 2025 at 03:01 by WorkflowHub Bot

Updated to v1.0beta3


Frozen v1.0beta3 22438d9

v1.0beta2 Created 29th Mar 2025 at 03:01 by WorkflowHub Bot

Updated to v1.0beta2


Frozen v1.0beta2 7444f24

v1.0beta1 (earliest) Created 29th Mar 2025 at 03:01 by WorkflowHub Bot

Updated to v1.0beta1


Frozen v1.0beta1 22269e3
help Creators and Submitter
Creators
Submitter
Tools
gfastats
seqtk
Minimap2
DeepTools
License
MIT License (MIT)
Activity

Views: 3136   Downloads: 4839   Runs: 0

Created: 29th Mar 2025 at 03:01

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